International Journal of Remote Sensing

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Using MERIS data to assess the spatial and

temporal variability of phytoplankton in coastal
areas

J.M. Beltrán-Abaunza, S. Kratzer & H. Höglander

To cite this article: J.M. Beltrán-Abaunza, S. Kratzer & H. Höglander (2017) Using MERIS data to
assess the spatial and temporal variability of phytoplankton in coastal areas, International Journal
of Remote Sensing, 38:7, 2004-2028, DOI: 10.1080/01431161.2016.1249307

To link to this article: https://doi.org/10.1080/01431161.2016.1249307

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INTERNATIONAL JOURNAL OF REMOTE SENSING, 2017
VOL. 38, NO. 7, 2004–2028
http://dx.doi.org/10.1080/01431161.2016.1249307

Using MERIS data to assess the spatial and temporal

variability of phytoplankton in coastal areas
J.M. Beltrán-Abaunza, S. Kratzer and H. Höglander
Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden

ABSTRACT ARTICLE HISTORY

This study aims to highlight how satellite data can be used for an Received 15 December 2015
improved understanding of ecological processes in a narrow Accepted 10 October 2016
coastal bay. The usefulness of the Medium Resolution Imaging
Spectrometer (MERIS) data (2003–2011) as a complement to the
in situ monitoring in Himmerfjärden (HF) bay is used as an exam-
ple that can also be applied to other coastal areas. HF bay is one of
the most frequently monitored coastal areas in the world, allowing
for a rigorous comparison between satellites and ship-based mon-
itoring data. MERIS data was used for the integration of chloro-
phyll-a (chl-a) over each waterbody in the HF area, following the
national waterbody classification by the Swedish Meteorological
and Hydrological Institute (SMHI). Chl-a anomaly maps were pro-
duced for the bay and its adjacent areas. The maps could be used
to show events with high chl-a, both with natural causes (e.g. a
Prymnesium polylepis bloom observed in summer 2008) and of
anthropogenic causes (e.g. failure in the local sewage treatment
plant resulting in a strong spring bloom in 2006). Anomaly maps
thereby allow to scan larger coastal stretches to discriminate areas
that may require additional sampling by ship, or to identify areas
that do not differ much from the median value of the MERIS time
series.

1. Introduction
Eutrophication, causes degradation of water quality, affecting the health and function-
ing of aquatic ecosystem worldwide, especially in coastal waters and estuaries (Nixon
1995). Due to nutrient enrichment, eutrophication is also the most serious pollution
problem for Baltic Sea ecology (Ahtiainen et al. 2014; Boesch et al. 2006). Point sources
(i.e. wastewater and riverine inputs) and diffuse sources (i.e. agricultural runoff and
fertilizers) have increased nutrient concentrations and reduced water quality by promot-
ing excessive algal blooms, increasing suspended organic material and thus lowering
water transparency (Savage, Leavitt, and Elmgren 2010). Significant reductions in nutri-
ent inputs from point sources over the past 35 years has shown only limited signs of
improvement in the Baltic Sea Proper (Ahtiainen et al. 2014; Boesch et al. 2006).

CONTACT S. Kratzer Susanne.Kratzer@su.se Department of Ecology, Environment and Plant Sciences,

Stockholm University, Stockholm, Sweden
© 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://
creativecommons.org/licenses/by-nc-nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided
the original work is properly cited, and is not altered, transformed, or built upon in any way.
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2005

Since the 1970s there have been ship-based, conventional monitoring programmes
that perform frequent measurements in coastal areas for evaluation of water quality
parameters, such as chlorophyll or suspended particulates concentrations, nutrients and
many others. However, in situ sampling methods are discrete, and limited in time and in
space. The spatial coverage and frequency of observations are usually compromised by
the high costs involved to produce the measurements, and may not fully represent the
condition of the entire waterbody.
Ferrybox observations have increased the spatiotemporal coverage of phytoplankton
biomass by taking fluorescence measurements of chlorophyll-a (chl-a) and phycocyanin,
and thus providing a detection of natural variability in phytoplankton (Rantajärvi et al.
1998). Ferrybox measurements usually have a sampling interval of about 20 s, which
corresponds to about 200 m distance between measurements. The measurements have
been successfully used for the delineation of cyanobacterial blooms (Groetsch et al.
2014). However, these measurements are spatially limited to the ferry route line.
Currently, a major focus has been on the spatiotemporal mapping of algal blooms
using satellite data, in order to cover the need of more effective environmental mon-
itoring in coastal areas (Blondeau-Patissier et al. 2014a). Here, visible spectroradiometry
of the sea (i.e. ocean colour remote sensing) provides an alternative method of water
quality monitoring over much greater spatial extents and with much higher frequency,
and at a much lower costs when compared to conventional surveys (Platt and
Sathyendranath 2008).
Ocean colour datasets can be combined to produce a composite image representa-
tive of the conditions over the period for which it was constructed (so-called level 3
products). The temporal resolution of such composite images can be either weekly
(minimum), monthly (Kratzer, Harvey, and Philipson 2014), or yearly in order to look at
long-term trends and inter-annual seasonal changes in ecological indicators (Platt and
Sathyendranath 2008; Racault et al. 2014).
The reliability of satellite-derived chl-a retrievals in the coastal zone, have improved
substantially with the second generation of ocean colour sensors, such as the Medium
Resolution Imaging Spectrometer (MERIS) which operated from 2002 to 2012. MERIS,
developed by the European Space Agency (ESA) and launched on the ENVISAT satellite,
was especially adapted for coastal applications. It had a high spatial resolution
(290 m × 260 m) and 15 spectral channels in the visible and near-infrared region
(Doerffer, Sorensen, and Aiken 1999). MERIS has shown to be a very powerful tool to
assess coastal marine and fresh-water ecosystems (McClain 2009; Odermatt et al. 2012a)
and it is also increasingly used as tool for coastal management and monitoring of algal
blooms (Blondeau-Patissier et al. 2014b; Gómez, Alonso, and Garca 2011; Harvey, Kratzer,
and Philipson 2015; Odermatt et al. 2012b). Although, the communications with the
ENVISAT satellite was lost in April 2012, and hence transmission of MERIS data was no
longer possible, there is a legacy of 10 year satellite data archive to be exploited (Laur
2012), which can be used for further algorithm improvements and refinements.
Furthermore, the Sentinel-3 operational mission was successfully launched on 16
February 2016, and thus continues the legacy and methods established by the MERIS
mission. The Ocean & Land Color Instrument (OLCI) on Sentinel-3 is designed with the
same spectral bands and radiometric performances as MERIS, plus six additional bands,
in order to cover a range of 400–1020 nm (Regner 2013) and to improve the
2006 J. M. BELTRÁN-ABAUNZA ET AL.

atmospheric correction procedures and the retrieval of water quality products in coastal
waters.
Previous research has shown that MERIS data can be used to monitor coastal areas in
the Baltic Sea and that the concentration of chl-a can be derived reliably despite the
high absorption by yellow substances (Kratzer, Brockmann, and Moore 2008; Vaičiūtė,
Bresciani, and Bučas 2012; Attila et al. 2013; Beltrán-Abaunza, Kratzer, and Brockmann
2014; Harvey, Kratzer, and Philipson 2015).
The aim of this study is to demonstrate how satellite-derived data can be used to
describe and improve the knowledge about the spatial and temporal variability of
phytoplankton biomass (as chl-a) in coastal areas. The Himmerfjärden (HF) bay and
adjacent areas in the NW Baltic Sea are used as an example in this study. HF has
experienced deliberate experiments with changes in nutrients loads from a sewage
treatment plant as part of management since 1984 (Elmgren and Larsson 2001b;
Savage, Elmgren, and Larsson 2002; Savage, Leavitt, and Elmgren 2004, 2010; Franzén
et al. 2011; Larsson et al. 2015). The bay, therefore, represents a unique opportunity to
study the variability of water quality as it has been monitored long-term by SYVABs
marine monitoring programme (HF Eutrophication Study) and the Swedish National
Marine Monitoring Programme.

2. Methods
2.1. Study area
HF bay in the southern Stockholm archipelago is a north–south facing elongated bay of
about 30 km length and 4 km width. It acts as recipient for the HF sewage treatment
plant which is located in the head of HF bay (Figure 1). The plant is the third largest
sewage treatment plant in the Stockholm region, serving approximately 300,000 people
from the southern Stockholm area. The bay is one of the most monitored areas in the
world (Elmgren and Larsson 2001a,b; Zakrisson, Larsson, and Höglander 2014) and the
regular measurements go back to the early 1970s.
The bay has been used for a series of full-scale adaptive management experiments in
the Himmerfjärden sewage treatment plant (HSTP). From 2007 to 2010, a nitrogen
experiment was carried out in the sewage plant to study the effects of nitrogen release
on eutrophication, and on the development of phytoplankton and cyanobacteria
blooms. The experiment entailed effluent release without nitrogen treatment during
2007–2008, and with full capacity nitrogen treatment during 2009–2010 but outlet
moved to 10 m instead of 25 m deep (Franzén et al. 2011).

2.2. Data sources

2.2.1. Chl-a, in situ data
Two ship monitoring datasets were available for this study: sampled at station B1 from
the Swedish EPA’s National Marine Monitoring Programme and from stations H3, H4,
and H5 in Himmerfjärden, sampled within SYVAB’s marine monitoring programme
(Himmerfjärden Eutrophication Study). The stations were sampled 22 times per year
2002–2012 (monthly January–February and November–December; weekly between mid-
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2007

Figure 1. Himmerfjärden (HF) bay and adjacent areas with the different waterbodies indicated by
different colours. Each colour refers to an individual waterbody ID, defined and assigned by the
Swedish Meteorological and Hydrological Institute and provided as shapefile (Havsomr_y_2012_2).
The monitoring stations are represented by circles, and the location of the sewage treatment plant
outlet is indicated by a square (HSTP). The focus of this study are waterbodies 7, 9, and 20, which
constitute a clear gradient in water quality from the inner bay (7) to the outer bay (9) and the
reference waterbody (20) just outside HF bay.

March to mid-May and every second week during the rest of the year). The sampling
depth for chl-a was 0–20 m at station B1 and 0–14 m (integrated hose samples) at the
other stations. Additional surface samples were provided for station H4. Concentrations
of chl-a were provided by SYVABs marine monitoring programme (Himmerfjärden
Eutrophication Study, http://www2.ecology.su.se/dbhfj/index.htm) for the years
2002–2012 and stations H5, H4, H3 and from the Swedish National Monitoring
Programme for station B1 (Figure 1).
Two litres of vertically integrated-hose samples, or two litres of surface samples
(station H4) were filtered onto GF/F filters. Chl-a was extracted from the filters which
were ground in 90% acetone (2002–2010) or ethanol (2011–2012), stored for 6–12 h in a
refrigerator and subsequently analysed for chl-a using a spectrophotometer (SIS-stan-
dard SS028146).

2.2.2. Satellite data

The MERIS full resolution (FR, that is, 300 m spatial resolution) archive covering the
full mission of the ENVISAT satellite (2002–2012) was acquired for the study area. As
ENVISAT was launched in March 2002 and ceased working in March 2012, the years
2002 and 2012 (during the start and ending of the ENVISAT Mission) were not fully
2008 J. M. BELTRÁN-ABAUNZA ET AL.

covered by MERIS, and to avoid bias in the dataset, the data from those years was
therefore not included in the subsequent chl-a analysis. MERIS passed these lati-
tudes about 2–3 times per week, but when there was cloud cover no images were
available as visible light is fully attenuated by clouds. The total field of view of MERIS
is 1150 km (swath width), and MERIS collected data for the entire planet every
3 days.
ENVISAT standard products that can be delivered to the public may include three
types of processing levels (ESA 2006):

● Level 1b products are geolocated data with pixel values calibrated to match the
Top of Atmosphere (TOA) radiance.
● Level 2 products are data derived from the level 1b data, with pixel values
processed to get geophysical measurements, for example algal pigments concen-
trations (chlorophyll-a), suspended particulate matter (SPM), etc.
● Level 3 products are synthesized from level 2 products and are often of a reduced
spatial resolution (e.g. 4 km resolution) and are often averaged over a certain
period of time; i.e. weekly, monthly, or yearly averages.

Here, an enhanced level 1b archive was provided by the CoastColour project

http://www.coastcolour.org/. This dataset consisted of MERIS FR (2nd reprocessing)
so-called level 1p products (version 1.6.3). The differences of CoastColour level 1p
(CCL1P) products compared to the standard level 1b products (v.3) are that CCL1P
products have been pre-processed with AMORGOS (ACRI-ST 2011a), providing accu-
rate geolocation information for each pixel. Then a radiometric correction was
applied, providing similar quality as the MEGS standard level 1b products from the
third reprocessing (ACRI-ST 2011b). Then the CCL1P processing was followed by smile
correction, equalization of coherent noise and an additional pixel classification step
(Ruescas et al. 2014). This classification also includes information on a precise coast-
line and it was also reformatted into NetCDF format, following climate forecast (CF)
conventions.

2.2.3. Pre-processing
The CCL1P datasets were batch-processed using the Earth Observation Toolbox and
Development Platform (BEAM, version 4.10.3) software. The batch-processing included
correction for adjacency effects using the Improved Contrast between Ocean and Land
(ICOL+, Santer and Zagolski (2009)). The geophysical products (level 2 processing) were
derived from the WeW Water Processor developed by the Free University of Berlin (FUB;
(Schroeder et al. 2007; Schroeder, Schaale, and Fischer 2007). This processor is readily
available as plug-in in BEAM. The data validation object of the chosen processing chain
are described in more detail in the works of Beltrán-Abaunza, Kratzer, and Brockmann
(2014) and Ruescas et al. (2014).
Note that in waterbodies with a predominant geomorphology where the most
dominant adjacency effect is in the direction of the forward scattered sun–light (i.e.
the direction where the sun is), like in HF (south–north facing), ICOL may be more
successful in removing the effects from reflectance from land as ICOL is working in the
principal plane (Santer and Zagolski 2009).
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2009

Table 1. Quality flagging applied to MERIS datasets.

CoastColour flags (level 1p)
CC_LANDa Flags land pixels
CC_COASTLINEa Flags the coast line
CC_CLOUDa Flags cloud pixels
CC_CLOUD_AMBIGUOUSa Flags potential cloud pixels
CC_SNOW_ICEa Flags snow & ice pixels
CC_MIXEDPIXELa Flags mixed pixels
CC_GLINTRISKa Indicates risk of sun glint
FUB processor specific flags (level 2)
LEVEL1b_MASKEDb General mask
CHL_INc, CHL_OUTb Indicates if chl-a concentration is within training range
a
All products.
b
All water products.
c
Only algal_2 product from FUB.

2.2.4. Quality control of water products

The FUB processor was used to derive the algal pigments (algal_2 product), as a proxy of
the chl-a concentration. Quality datasets were produced by masking out pixels that
raised the set of conditions described in Table 1. A combined logical mask also excluded
any invalid pixel values such as negative values.
Furthermore, using the frequency of occurrence of valid pixels after applying the
combined mask, a spatial data density mask was created. Pixels that occurred less than
300 times in the time series, were masked out.

2.2.5. Level 3 processing

Composite images with both weekly and monthly temporal resolution were created by
pixel-wise averaging of non-flagged pixels to reduce the influence of missing pixels due
to cloud cover or low quality data identified by the combined data quality masks. This
set of composite images constitutes a time series of high quality data, where every pixel
in each image represent a binned value, on the basis of which seasonality metrics can be
derived.
Note that the spatial relationship is preserved and can be used for further analysis. A
shape file (Havsomr_y_2012_2) from the Swedish Meteorological and Hydrological
Institute (SMHI), representing the waterbodies in the study area was used to spatially
aggregate the satellite-derived products.

2.3. Data processing

2.3.1. Hovmöller diagrams
Next, the weekly composites were spatially aggregated per waterbody. A minimum of
25 quality pixels per waterbody were set as minimum requirement, and their descrip-
tive statistics were calculated. Hovmöller diagrams (Hovmöller 1949; Hocke and
Kämpfer 2009) of the chl-a concentration were created for the waterbodies 7, 9,
and 20, representing an optical gradient from the outlet of the Himmerfjärden
sewage treatment plant (waterbody 7, including stations H5 and H4, see Figure 1),
to the outer bay (waterbody 9, station H3), and towards the open sea (waterbody 20,
station B1, see Figure 1). The squares in the Hovmöller diagram contain the mean
value of all the valid pixels within a given waterbody. The weekly time series
2010 J. M. BELTRÁN-ABAUNZA ET AL.

composite data is displayed in columns and the yearly data in rows. The timing of
spring phytoplankton growth derived from in situ data (i.e. the week number when
the chl-a concentration reaches its maximum) was overlaid on the corresponding
squares of the Hovmöller diagrams.
The initiation and termination of the phytoplankton growth periods measured in situ
were also plotted onto the Hovmöller diagrams. These ecological indicators were based
on the threshold method (Siegel, Doney, and Yoder 2002; Platt and Sathyendranath
2008; Platt et al. 2009) which was set to 5% of the yearly-median value. The values for
the latter were estimated by detecting the week number at which its relative change
crosses the threshold line.

2.3.2. Comparison to monitoring data

Next, the SMHI-defined waterbodies were overlapped to form spatial composites of
waterbody classes. Within each waterbody class, all pixel values were averaged over a
week and relevant statistics were calculated. The aggregation of averaged waterbody
values were compared to data from the in situ sampling at station B1 (measured within
the Swedish National Marine Monitoring Programme) and at stations H3, H4, and H5
from SYVABs marine monitoring programme (HF Eutrophication Study).
A validation of the satellite data in the region of study was previously done by Kratzer
and Vinterhav (2010) and Beltrán-Abaunza, Kratzer, and Brockmann (2014) using differ-
ent algorithms that included the standard MEGS processor and the FUB processor, both
the adjacency correction and the performance of the processors were tested. The FUB
algorithm was found to retrieve chl-a concentrations most reliably with a bias range of
18–26% (Beltrán-Abaunza, Kratzer, and Brockmann 2014). A comparison between inde-
pendent methods for chl-a estimation between the national marine monitoring pro-
gramme and retrieved from MERIS was carried out by Harvey, Kratzer, and Philipson
(2015). They found a strong correlation between measurements from satellite-derived
chl-a compared to in situ measurements taken close in time (0–3 days), with a mean
normalized bias of 17% and root mean square errors of 65%. They also found that the
comparison of monitoring data with MERIS by monthly means reduced the mean
normalized bias to 8%.
In this study, the comparison aims to show the usefulness of MERIS in coastal areas
such as HF. Different ways of comparing satellite data with in situ data and how satellite
data can be used as a complement to in situ data are shown in the results. Although, due
to space limitations, only the results from station H4 over selected years were included
here.

2.3.3. Anomaly maps

Weekly and monthly climatology maps were calculated on a pixel-by-pixel basis, using
median values across the years. The week numbers calculated for each available date,
both in situ and satellite, followed the ISO 8601 standard for dates (see https://www.iso.
org/obp/ui/#iso:std:iso:8601:ed-3:v1:en). The anomaly maps were created as follows:
Ay ¼ Dy  C; (1)

where A is the anomalies dataset composite, either by weekly or monthly averages, over
the full year, y, ranged [2003–2011]. Only complete years were included in the
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2011

calculations, displayed with either weekly [1–52], or monthly increments [1–12]. The
dataset for the given year and composite is represented as D, and the climatology as C.

3. Results
3.1. Available MERIS data
Available MERIS data are those where the criteria of a minimum of 25 available pixels
(i.e. at least 25 pixels per waterbody) was met. In Figure 2, which uses waterbody 7 as an
example, the maximum number of available scenes per month are presented. There was
a normal distribution of available scenes for the period from February to November.
MERIS data was only available during February to November due to the low sun
inclination at such high latitudes in winter. For consistency in data coverage and data
analysis, only those 9 years that covered a full cycle from February–October were
included in the anomalies analysis (i.e. the years 2003–2011). February and November
on average had the lowest number of scenes per month, that is, 30 and 11 scenes,
respectively. This was an expected result, showing the influence of low sun altitude and
high frequency of cloud cover during the late fall and winter months. June clearly
showed the maximum number of available scenes, with a value of 89 during 9 years
of full coverage, that is, almost 10 scenes on average for the month June, and about 8
scenes per month for April, May, July, and August, which compares to weekly sampling
by ship during the spring bloom, and 2-weekly sampling during the summer bloom.
The weekly composites derived in the subsequent analysis, thus started from week 6
and covered the period until week 44.
For the entire MERIS time series (June 2002–April 2012) in the studied region about
2365 scenes were available. Only about 24% of the scenes, that is, 565, reached the
maximum occurrence of valid pixels for FUB-derived chl-a (see Figure 3(a)). The number
of available scenes was higher in the open sea areas when compared to the inner bay,
probably due to more clouds in coastal areas, aerosols that may contribute to atmo-
spheric correction failure and possibly due to land adjacency effects.

Figure 2. Maximum number of available scenes used to build the monthly climatology (2003–2011).
Here, waterbody 7 (inner HF bay) is shown as an example.
2012 J. M. BELTRÁN-ABAUNZA ET AL.

Figure 3. (a) Pixel availability for the entire MERIS archive (2002–2012) over Himmerfjärden. (b)
Coefficient of variation (CV) computed from monthly mean composites (March–October,
2003–2011).

The relative spatial distribution of chl-a during the period March–October is shown in
Figure 3(b) (using only years where the complete period March–October was covered
with data). Higher variability in chl-a was observed in waterbodies 7 and the outer part
of waterbody 9, as well as in waterbodies 8, 11, and 17 (Figure 3(b); for stations and
waterbody references see Figure 1). The open sea region close to station B1 in water-
body 20 and in waterbody 25 shows lower variation in chl-a concentration. The higher
variability at the outer part of waterbody 9 was most likely an effect of a strong chl-a
anomaly in spring 2006 (see Figure 4). It was notable that outside the bay there was a
corridor of low variability in chl-a concentrations including station B1 (Figure 3(b)), while
higher variability can be observed between 15 and 20 km offshore, corresponding to the
area most strongly affected by upwelling (Gidhagen 1987; Kratzer and Tett 2009).

3.1.1. Spatiotemporal chl-a anomalies in HF bay

Very few pixels were available in the inner HF bay in February and March 2006 and 2010
(Figures 4(a),(b),(g),(h)), probably due to the fact that the bay was ice covered during these
periods (unpublished data from HF Eutrophication Study). In February 2006, the only data
in the inner bay (Figure 4(a)) seems to correspond to the ice-free channel for boat
transports to the town of Södertälje (situated in the northern head of the bay). The reason
for the extremely high anomaly values of chl-a (about +47 mg m–3 above the monthly
median value) observed inside Himmerfjärden and along the coast during the winter
months of February and March for years 2006 and 2010 is likely to be ice cover. During
2008 in contrast, no significant ice cover was found in HF bay, and the positive anomalies
(chl-a values above the long-term median 2003–2011) were lower, that is, about +2.7 mg
m–3 (Figures 4(d) and (e)). Positive anomalies seems to form first in the open sea during
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2013

Figure 4. Monthly anomalies of chl-a concentration during spring (February–April) for the selected
years 2006, 2008, 2010. The value of maximum anomaly is shown in the upper right legend of each
plot. See also Appendix for complementary material, that is, maps of median values for spring and
the spatial distribution map of corresponding pixel-availability counts. See also Figure A1 in the
appendix showing median chl-a values for spring and pixel-availability counts.

March (years 2006 and 2010) and then the anomalies (Figure 4) are developed inside the
bay towards the head of the bay in April (waterbody 7, stations H5 and H4, Figure 1).
During 2008, negative anomalies were observed inside the bay during March and April
(Figure 4(e,f)). The negative anomalies were also found during this year in the open sea in
April and below −3 mg m–3 (Figure 4(f)) in waterbody 7, stations H5 and H4, see Figure 1.
2014 J. M. BELTRÁN-ABAUNZA ET AL.

During the summer months, two major chl-a anomalies (with higher chl-a than the
long-term median values) could be observed during June and July 2008 in the
Himmerfjärden inner bay (waterbody 7, Figures 5(d) and (e)). Mild positive anomalies
were observed also in August 2006 (waterbody 17, Figure 5(c)) and 2010 (waterbodies 7
and 6, Figure 5(i)). The observed anomaly in June 2010 (Figure 5(g)) in waterbody 20/21
was most likely an artefact caused by an airplane condensation trail (contrail), leaving a

Figure 5. Monthly anomalies of the chlorophyll a concentration during summer (June–August) for
the selected years 2006, 2008, 2010. The value of maximum anomaly is shown in the upper right
legend of each plot. See also Appendix for complementary material, that is, maps of median values
for summer and the spatial distribution map of corresponding pixel-availability counts. See also
Figure A2 in the appendix showing median chl-a values for summer and pixel-availability counts.
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2015

cirrus cloud that was not correctly flagged by the quality flags, due to its spectral
similarity to surface accumulations.

3.1.2. Temporal variability of chl-a

In order to illustrate the succession of phytoplankton blooms over the year using the
satellite-derived chl-a values for a specific area, Hovmöller diagrams were applied. In the
Himmerfjärden area the timing of the spring phytoplankton growth period was usually
between weeks 6 and 21 (Figure 6). The next major bloom period is in the summer when
the chl-a concentrations peaks again during the summer blooms when cyanobacteria
usually occur in the area (Zakrisson, Larsson, and Höglander 2014), usually between
weeks 22 and 34 (Figure 6). In between the spring and summer bloom period, when the
spring bloom phytoplankton has exhausted the nutrients after the spring bloom and
before the water temperature has increased to favour the summer phytoplankton
species (data not presented here), there was a period with low chl-a values clearly
shown in the Hovmöller diagrams (Figure 6). For the dynamics of temperature and
nutrient values for the stations H5, H4, H3, and B1, see the online SYVABs marine
monitoring programme available at http://www2.ecology.su.se/dbhfj/index.htm.

Figure 6. Hovmöller diagram of chl-a for selected waterbodies (7, 9, and 20; see Figure 1). Spring
maximum from monitoring data was shown as red/orange points over the square-cells of the
diagram (station H4 and H5 in waterbody 7, H3 in waterbody 9, and station B1 in waterbody 20).
The white triangles mark the start and ending week of the spring bloom from in situ data as a point
of reference. The week number refers to the week of the year.
2016 J. M. BELTRÁN-ABAUNZA ET AL.

Differences between areas can be visualized by comparing Hovmöller diagrams from

different areas. The chl-a values during the spring phytoplankton bloom are, for exam-
ple, higher in the inner bay compared to the more open sea areas (Figure 6).
The Hovmöller diagrams also illustrate differences between years, for example, the
exceptionally high chl-a values in waterbody 7 in summer 2008 (Figure 6), which is
consistent with the anomaly results observed in Figure 5 and can be used to visually
compare different waterbodies and years. Note that the number of scenes used to derive
the mean chl-a values can be found in Figure 7. Usually, there were between 2 and 4
scenes with at least 25 valid pixels aggregated in each waterbody. There were weeks
with only one scene providing the mean chl-a value for the waterbody. However, this
does not guarantee that in other areas of the image we would find valid pixels. Hence,
the anomaly maps were built up using monthly aggregates instead of weekly ones.
An example from 2010 (Figure 8) shows that this year the open sea reached peak chl-
a concentrations between weeks 12 and 13 according to MERIS data. In the middle of
the bay (around waterbody 9) the chl-a concentration reached its maximum during
weeks 13–15. Then, finally the head of the bay (waterbody 7), reached its maximum chl-
a concentration between week 14 and 17. The plane contrails shown in Figure 8, and
masked manually in white (also shown in Figure 5(g)) points out that the atmospheric
correction is not completely reliable as yet, as the cloud mask did not detect the

Figure 7. Hovmöller diagram showing the number of scenes used to derive the mean chl-a values
(Figure 6) for selected waterbodies (7, 9, and 20; see Figure 1). The week number refers to the week
of the year.
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2017

Figure 8. Spatial timing of the chlorophyll-a maximum during spring (March–May) 2010.

contrails. It is likely that this will be improved with the Sentinel-3 mission, as OLCI has
additional channels to improve atmospheric correction.

3.1.3. Comparison in situ and satellite data

Differences in the development of the spring bloom, using in situ and MERIS data, were
observed in Figure 6. The red and orange dots showed the timing of the maximum
spring bloom, in waterbody 7 in the inner HF bay, for the two in situ stations (H4 and H5,
respectively). Station H4 frequently falls within one week of difference to the observed
MERIS maximum chl-a value during spring for most years (visual comparison Figure 6).
Station H5 (orange points), peaks most frequently at the same time at H4, however was
shown that it could also peak from 1 to 3 weeks later than H4 (e.g. year 2005 in Figure 6
for this waterbody). Waterbody 9 in the middle of the bay and 20 open sea/coast,
showed an apparent disagreement with regards to the timing in the spring bloom,
between in situ and MERIS data, with the in situ chl-a often peaking 1–2 weeks after the
peak in MERIS data (Figure 6).
The white triangles mark the start and ending week of the spring bloom from in situ
data (Figure 6). By visual comparison with the MERIS underlying data of the Hovmöller
diagrams, a closer agreement was observed for the period range of phytoplankton
spring bloom with the colour gradients within waterbody 7 (station H4) compared to
in the waterbody 9 and 20 (Figure 6). The overlay of the ecological indicators (maximum
and period range of phytoplankton spring bloom) based on in situ data over the MERIS
data, showed, lower intensity spring blooms in waterbody 20 (station B1). Low intensity
2018 J. M. BELTRÁN-ABAUNZA ET AL.

spring blooms relative to summer blooms, may have been misinterpreted as non
existing in the Hovmöller diagrams by looking only at MERIS data, as the summer
blooms were observed to dominate the higher chl-a values for this outermost
waterbody.
Using station H4 as an example, Figure 9 shows a comparison between the data
measured in situ by the monitoring programme and the data derived from MERIS.
Although the spring bloom was lower in 2008 compared to 2006 and 2010 (both in
situ and MERIS data), the summer values were higher (Figure 9).
In general, the spring period usually lacks satellite data for some weeks, while the
summer period is usually better covered by satellite data (Figure 9). The in situ data in
this explicit example, however, are more frequent during spring than during the summer
(Figure 9). Due to this the spring chl-a peak might be missed in the satellite data, as in

Figure 9. Example of weekly averaged values for station H4 for selected years (2006, 2008, and
2010). Chl-a in situ hose data shown as blue squares, chl-a surface data shown as green circles.
Satellite data for waterbody is shown as boxplot using a minimum of 20 valid pixels for chl-a derived
from MERIS.
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2019

2008 (Figure 9), while the satellite data might give information between in situ sam-
plings during summer.

4. Discussion
The purpose to monitor a coastal area can be both to detect and to follow up natural or
anthropogenic changes in a coastal area. The need to follow national goals (as the
Swedish Environmental objectives) as well as international directives such as the EU
water framework directive as well as the HELCOM Baltic Sea Action Plan has lately
increased the need of monitoring data. Traditionally, monitoring has been achieved
through conventional in situ measurements (Moore et al. 2009). During the past three
decades (McKinna 2015), the use of other methods, such as satellites, mostly used in
open sea areas, has increased also in coastal areas as the methods to account for optical
parameters, such as chl-a, SPM and coloured dissolved organic matter (CDOM) have
largely been improved (IOCCG 2000; Gohin et al. 2008; Blondeau-Patissier et al. 2014a).
In this study we have used chl-a as an example to illustrate the spatiotemporal variability
of dynamical processes in a coastal area using the satellite data from the MERIS archive
and how it can be used as a complement to traditional in situ monitoring and vice versa.
Studies have shown examples of the exploitation of the MERIS archive to describe
phytoplankton bloom dynamics in optically complex waters (Palmer et al. 2015;
Blondeau-Patissier et al. 2014b; lakes and tropical regions, respectively). Remote sensing
combined with ferrybox observations in the Baltic Sea, reliable time series of water
quality maps have been produced (Groetsch et al. 2014; Fleming and Kaitala 2006). The
approach used here with HF bay as an example is distinct from most previous coastal
work, as this study benefits from the availability of a uniquely long and frequent in situ
time series. The study demonstrates effective use of the MERIS archive to produce
datasets with improved data quality by means of applying rigorous data density
masks (flagging) that help to remove pixels of low data quality and produce quality
base maps. Furthermore, the climatologies and anomaly maps produced here, may serve
as a reference to assess the accuracy of chl-a values on other ocean colour missions such
as the Sentinel 3.
Changes in the water column can be explored using chlorophyll a data. However,
methods differ on how phytoplankton bloom dynamics can be observed and evaluated.
A common practice is to use the definitions of ecological indicators given by Platt et al.
(2009) and Racault et al. (2014). Basically, the phytoplankton phenology uses here the
date when the chlorophyll-a concentration (usually based on weekly aggregates) rises
above, or falls below, a threshold value usually representing the median background
value. Note that these thresholds are region-specific (Palmer et al. 2015).

4.1. Comparison in situ and satellite data

When comparing monitoring in situ data with satellite data for station H4 in the inner HF
bay (Figure 9) a better data agreement could be observed in years 2006 and 2010,
compared to the year 2008. In 2008, the discrepancies were overall much higher and
more frequent. Such discrepancies may be due to the temporal weekly mean data
aggregation of satellite data integrated over the whole waterbody, which is then
2020 J. M. BELTRÁN-ABAUNZA ET AL.

compared to a single in situ sampling point from the same week. It is assumed that
stations within each waterbody share similar biophysical characteristics, using the SMHI-
defined waterbodies. The spatial and temporal dynamics of phytoplankton showed the
need to use a complementary characterization of the waterbodies, as their spatial-
averaged-data-aggregation may smooth out areas of higher variability. Therefore, it is
recommended to use both, the images showing the spatial variability at pixel-level
(Figures 4, 5, and 8) along with the Hovmöller diagrams, to aid in their interpretation.
In Figure 9, in situ values of chl-a from both surface and integrated hose sample (0–
14 m) were compared with the satellite data that integrates the chlorophyll-a values to
just below the Secchi depth (which ranges from about 2–5 m in the bay). Rather low
Secchi depths values were measured in a bio-optical cruise in July 2008, with an average
Secchi depth of only about 3 m in Himmerfjärden bay, and only around 2 m at stations
H4 and H5 (Kratzer and Vinterhav 2010), which may have affected the satellite retrievals
by reducing the reflectance received by the satellite. The surface in situ values were also
more close to the satellite values compared to the integrated hose samples (Figure 9).
Despite the discrepancies between satellite and in situ data, MERIS can give information
about bloom events occurring in-between in situ observations, showing a peak value
around week 26 in 2006 that was not observed in the in situ time series (Figure 9).
The in situ chl-a was sampled both with a hose, and therefore represents a vertically
integrated sample (0–14 m) and with samples from surface. Both, hose and surface chl-a
values follow the same pattern as MERIS values boxplots, but when comparing hose and
surface chl-a, the latter was often higher (Figure 9). During the summer months of 2008,
between week numbers 21 and 34, the agreement of the in situ data and MERIS, is
almost zero (Figure 9). There is a lot of variability in the MERIS values that are also higher
than the in situ chl-a measurements. This is presumably due to the high horizontal
heterogeneity in waters dominated by cyanobacteria, which makes a direct comparison
of the two methods almost impossible. A water sampler only samples 5 l of water,
whereas the satellite views several millions of litres of water in a single pixel. So, there is
a clear difference in spatial dimensions of the two methods. It may be assumed, though,
that the satellite method gives a more representative picture of the natural environment
and the relative spatial gradients, whereas a water sample may be strongly biased as it
may not be spatially representative at all. The validation results from the NW Baltic Sea,
however, show that the FUB processor usually overestimates the chl-a concentration by
about 25% (Kratzer and Vinterhav 2010; Beltrán-Abaunza, Kratzer, and Brockmann 2014).
Note that in these validation activities, one aims at sampling in waters devoid of algal
blooms and/or strong surface accumulations of cyanobacteria in order to avoid the
problems that are caused by horizontal heterogeneity. The best scenario for a compar-
ison of satellite and in situ data is a homogenous surface mixed layer. Thermal stratifica-
tion in summer combined with Coriolis effects and coastal upwelling will most likely lead
to a heterogenic distribution of algal biomass in surface layers as shown in some of the
images.
Physical processes, such as the horizontal and vertical transport of phytoplankton
chlorophyll that drives the patchiness occurrences of phytoplankton blooms are the
most likely explanation for the discrepancies between the in situ and satellite data,
under the assumption that the water products were estimated successfully after the
atmospheric correction with an adequate optical model of the waterbody.
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2021

Phytoplankton processes and their structures can occur at the surface, below the surface
or even at greater depths (Klemas and Yan 2014). In situ sampling cannot reproduce the
natural spatial patterns of chlorophyll, as often the chlorophyll values are not represen-
tative of the spatial mean of this parameter (Vos et al. 2003). Remote sensing provides a
good estimation of the spatial mean values, however they can only estimate surface and
subsurface up to the first optical depth as can be seen in Figure 9. Therefore, in situ data
is a fundamental requirement for ocean colour products validation and for confirming
the reliability of the satellite products. However, through the coordinated use of both
types of data, an effective monitoring system of coastal water quality can be achieved
(Gohin et al. 2008).
Currently, the ecological status of phytoplankton in Swedish Baltic proper coastal
waters (according to the EU Water Framework Directive WFD) is classified according to
the surface chl-a concentration and the total biomass of phytoplankton measured as
biovolume (HVMFS 2013). In the Gulf of Bothnia and in Kattegat and Skagerrak hose
samples 0–10 m of chlorophyll-a are instead used (HVMFS 2013). The discrepancies
between the areas were due to the fact that more surface chl-a data was available
compared to integrated hose data when the assessment system for phytoplankton was
developed for the Baltic Proper (Larsson et al. 2006). The availability of chl-a values from
different in situ monitoring programmes will, therefore, also govern if surface or hose in
situ data can be used in the comparisons between satellite data and existing in situ
measurements.

4.2. Spatiotemporal chlorophyll a anomalies in Himmerfjärden bay

According to historical information about nitrogen removal at the Himmerfjärden
Sewage Treatment Plant (Larsson et al. 2014), the nitrogen removal was incomplete
during February to mid-May 2006, due to technical problems in the HSTP causing higher
loads of nitrogen to the bay, feeding a large spring bloom of phytoplankton. This may
have contributed to the strong anomaly observed in April 2006 (Figure 4(c)), with chl-a
values 10 mg m–3 above normal conditions. However, during spring 2008, no such
anomalies were observed, although this was a year with no nitrogen removal in the
HSTP due to the ongoing full-scale experiment in HF bay (Larsson et al. 2014).
The observed discrepancies during spring between the years could be explained by
sea ice melting during 2006 and 2010, which may have favoured the growth of
phytoplankton these years. In such conditions the water column may experience rapid
stratification due to the rapid supply of fresh water to the sea surface (Park et al. 2014).
The melting sea-ice thus provides vertical stability and increase nutrient supply in the
photic zone (Qu 2015), therefore a strong spring bloom may arise as shown in April 2006
and in 2010 (Figure 4). The strongest anomaly in satellite data in April 2010 occurred in
an area (waterbody 1, 12, 16, and 17) where no in situ measurements were available and
could therefore not be compared with in situ data.
The chl-a anomalies in summer 2008 in the inner HF bay (Figures 5(d)and (e)) may
suggest that the ongoing experiment, with high amounts of nitrogen released, stimu-
lated the development of phytoplankton blooms, and thus high biomass in this area.
The chl-a in situ measurements were also higher during that year compared to the long-
term mean (HF Eutrophication Study). But this was not the only reason for the high chl-a
2022 J. M. BELTRÁN-ABAUNZA ET AL.

values. At the same time a bloom of the phytoplankton group Prymnesiales (including
Prymnesium polylepis) was observed (Hajdu, Gorokhova, and Larsson 2015), a bloom that
occurred in large parts of the Baltic Proper from autumn 2007 to summer 2008 which
was probably the cause for the chl-a anomalies in June and July 2008 (Figure 5), and the
high chl-a values recorded by satellite (Figures 5 and 9).
If anomaly maps of chlorophyll-a repeatedly show anomalies in an area or for a long
period of time, this clearly indicates that something unusual is happening in the
respective area. Anomaly maps thereby allow to scan larger coastal stretches to dis-
criminate areas that may require additional in situ sampling, or to identify areas that do
not differ much from the median value of the MERIS time series. The in situ samples as
well as knowledge about the studied area could then help to reveal why there is such an
anomaly and thereby improve the interpretations of the satellite data. Alternatively, it
may be possible to see which coastal areas are rather homogeneous both in time and
space and maybe do not require such frequent in situ sampling.
How a monitoring programme is designed is also dependent on what one wants to
monitor and how variable the monitored parameter is in the studied area. Anomaly
maps as well as Hovmöller diagram were used to visualize chl-a data both on a spatial
and temporal scale to highlight when bloom events usually occurs or not (Figures 4–6).
Satellite data seems to perform better during the late part of the spring and during the
summer compared to the early spring (due to more clouds during spring and due to ice
occurrence). Snow and ice was for example masked in this study (as in spring 2006 and
2010, Figure 4) and tend to decrease the availability of data during cold winters
compared to warm winters (as 2008, Figure 4) when more data was available. When
comparing satellite data from different years knowledge about weather, ice, tempera-
ture as well as in situ measurement can be used to complement the satellite data in
times when the satellite data are infrequent, as during the spring. As in this example
when a frequent in situ programme during spring (weekly sampling) increases the
information about the spring period, while on the opposite the satellite data give
more information about the summer period when only every second week is sampled.

5. Conclusions
This article focused on the mapping of phytoplankton dynamics in a coastal area by
means of satellite remote sensing. HF bay is one of the most well monitored coastal
areas in the world but it lacked a comprehensive remote sensing study spanning over a
longer period of time and providing information on the spatial and temporal variability
of chl-a concentration. The methods demonstrated here (Hovmöller diagrams and
anomaly maps) are likely to become an important complement to the in situ monitoring
efforts in coastal areas in general, but also specifically in the Baltic Sea. The advantage of
the methods lies in the good spatial and temporal coverage as demonstrated in this
study.
The spatiotemporal information provided here may be used to locate those coastal
areas where additional in situ sampling may be required, or where it may be redundant.
It can also be used to evaluate how representative an in situ sampling station is for a
given waterbody. Using the presented methodology with improved data quality mask-
ing it is possible to enhance the data quality of satellite data, not only for MERIS but also
 INTERNATIONAL JOURNAL OF REMOTE SENSING 2023

for future missions, as the newly launched Sentinel-3. By combining remote sensing and
in situ sampling, it is possible to identify coastal areas that may have to be monitored
more frequently. In this study, chl-a was used as an example but it could also be used to
follow and implement monitoring of other parameters that can be derived from satellite
data, that is, Secchi depth, CDOM, SPM, and turbidity.

Acknowledgements
Acknowledgements to Brockmann Consult for the CoastColour L1p datasets used in this study.
Thanks to the NANSEN International Environmental Remote Sensing Center (NIERSC). To Ulf
Larsson and Jakob Walve (Department of Ecology, Environment and Plant Sciences, Stockholm
University) for providing access to the in situ time series of chl-a measurements done in HF within
the SYVAB marine monitoring programme (Himmerfjärden Eutrophication Study) and the Swedish
National Marine Monitoring programme. To Ragnar Elmgren from Stockholm University,
Department of Ecology, Environment and Plant Sciences, for valuable contributions regarding
the Swedish National Monitoring Data and descriptions of the Himmerfjärden Sewage treatment
plant nitrogen experiments. Thanks also to two anonymous reviewers for their suggestions to
improve this article. Thanks to ESA and ACRI-ST for developing ODESA, available at http://earth.eo.
esa.int/odesa.

Disclosure statement
No potential conflict of interest was reported by the authors.

Funding
This research was funded by the Swedish National Space Board [Dnr. 165/11] and the European
Space Agency [ESA, contract no. 21524/08/I-OL], by the FP7 projects WaterS and EuRuCAS and by
Baltic Ecosystem Adaptive Management (BEAM), a Swedish strategic marine project based at
Stockholm University; NordForsk [NordAquaRemS reference number 80106, NordBaltRemS refer-
ence number 42041]; Seventh Framework Programme [EuRuCAS, project number 295068,WaterS,
project number 251527].

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Appendix

Figure A1. Maps of median chlorophyll-a values for spring and the spatial distribution map of
corresponding pixel-availability counts (2003-2011).
2028 J. M. BELTRÁN-ABAUNZA ET AL.

Figure A2. Maps of median chlorophyll-a values for summer and the spatial distribution map of
corresponding pixel-availability counts (2003-2011).