Indicator Assessment

Chlorophyll in transitional, coastal and marine waters

Indicator Assessment
Prod-ID: IND-18-en
  Also known as: CSI 023
Published 06 Jul 2011 Last modified 11 May 2021
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  • In 2008, the highest summer chlorophyll-a concentrations were observed in coastal areas and estuaries where nutrient concentrations are high, namely in the Gulf of Riga, the Gulf of Finland and along the coast of France and Belgium.
  • Although nutrient concentrations in some European sea areas decreased from 1985 to 2008 (see Core Set Indicator 21), these changes were not clearly reflected in chlorophyll-a concentrations: of the 546 stations reported to the EEA the majority of the stations (89%) indicated no statistically significant change.
  • Changes were detected mainly in Finnish, Dutch, Norwegian, Swedish and Italian coastal waters. At the Finnish and Swedish monitoring stations chlorophyll-a concentrations showed both decreasing and increasing trends, whereas in Italy, Netherlands and Norway concentrations were mainly decreasing.
  • An analysis of changes based on satellite imagery show significantly increasing trends of ocean colour (equivalent to chl-a)along the Mediterranean coast, whereas trends are significantly decreasing in large parts of the central Mediterranean and Black Seas. It also shows significantly increasing trends in the Baltic Sea, but here the analysis is less certain.


Chlorophyll-a concentrations in European seas, 2008

Note: Chlorophyll-a concentrations in European seas in 2008 based on observations

Data source:

Baltic Sea

In 2008 the highest measured summer chlorophyll-a concentrations (> 6 µg/l) were found in the Gulf of Riga and in the Gulf of Finland. The Gulf of Riga is influenced by nutrient fluxes from the River Daugava, and with low dilution due to restricted water exchange with the Baltic Sea. In the Gulf of Finland, high concentrations are linked to the circulation that moves nutrient rich waters originating from the River Neva and St. Petersburg along the Finnish coast. Low concentrations (<2 µg/l) are predominantly observed in the Bothnian Bay, and in the Kattegatt.

Most of the stations (86%) did not show any change in chlorophyll concentration in the period 1985-2008. Positive changes were, however, observed: chlorophyll concentrations decreased in the Finnish coastal areas of the Bothnian Bay (at one third of the Finnish monitoring stations). In total statistically significant decreasing trends were evident at 6% of the Baltic Sea stations.  In contrast, increases were observed in the Gulf of Finland and at Swedish stations in the northern Baltic Proper. The latter result is in agreement with a recent study (Fleming-Lehtinen et al. 2008), which shows that chlorophyll concentrations increased in the Northern Baltic Proper in the period 1979 to 2006. In total, statistically significant increasing trends were evident at 8% of the Baltic Sea stations.

In recent years the Baltic Sea has suffered from frequent and extensive summer blooms of cyanobacteria, which colour large areas of the sea surface bright green or brownish yellow and are a nuisance to swimmers because they are slightly toxic. Cyanobacterial blooms are intermittent, occurring during calm meteorological conditions  and when phosphorous is available from occasional upwelling of deep water (Vahtera et al. 2007). Such conditions were predominant during 2008, where large areas of the Baltic Sea were covered by cyanobacterial blooms in July.

In general eutrophication is of major concern in the Baltic Sea and there are many initiatives, including the Baltic Sea Action Plan, that work towards reducing eutrophication.

 North Sea

Only limited amount of chlorophyll data of the North Sea was submitted to the EEA by the member states for the year 2008. The data coverage was best in coastal waters of France, Belgium, and in the Skagerrak. The highest summer chlorophyll-a concentrations (> 5 µg/l) were observed along the coast of France and Belgium. These areas have suffered from frequent blooms of Phaeosystis, which causes harm to recreational use of coastal waters by producing foam.

The majority of stations (90%) did not show any statistically significant change in chlorophyll concentration between 1985 and 2008. In a recent eutrophication report OSPAR (2008) stated that further efforts are still needed to reduce nutrient inputs otherwise the aim of the OSPAR Eutrophication Strategy - a healthy marine environment where eutrophication does not occur - will not be achieved. 

NE Atlantic

The highest concentrations were found in the French estuaries (> 10 µg/l). In the north eastern Scottish coastal waters chlorophyll concentrations varied from low (< 1.5 µg/l) to high (> 6 µg/l) depending on the location of the monitoring stations. OSPAR (2008) has defined some small coastal embayments and estuaries within the Celtic Seas and the Bay of Biscay and Iberian Coast as problem areas with regard to eutrophication. Harmful algal blooms of various species are observed occasionally in the NE Atlantic, but there is no evidence that the blooms would become more frequent in recent decades (Smayda 2006, Gowen et al. 2008). No significant changes in chlorophyll concentrations were observed.

Mediterranean Sea

The highest summer chlorophyll-a concentrations (> 5 µg/l) were in the French coastal water. No offshore data of the Mediterranean chlorophyll concentrations has been submitted to the EEA for the year 2008. The open water of the Mediterranean Sea is, however, poor in nutrients and thus summer chlorophyll-a concentrations are also low. The most eutrophic waters in Mediterranean are along the northern coastline, but eutrophication problem has been increasing gradually over the last decades also in the southern shore of the sea (UNEP 2007). Harmful algal blooms have been observed commonly in the northern coastal areas. These blooms have also consisted of dinoflagellates (e.g. Dinophysis and Alexandrium) potentially causing different types of shellfish poisoning (Koukaras and Nikolaidis 2004, Bravo et al. 2008).

Only France, Italy and Croatia have submitted long enough time series to estimate trends. Croatian observations start from the year 1998 and no changes could be detected. In Italian coastal waters summer chlorophyll-a concentrations were decreasing at 6%, increasing at 2% of the stations, and no statistically significant trend can be detected at the remaining 92% of stations. Decreasing trends were found in many different areas of Italian coast, but they were concentrated especially in the Gulf of Venice and the estuary of the Po River.

The ocean colour trend analysis has been used to support the analysis based on in-situ observations. In general significantly increasing trends are found in coastal waters of the Mediterranean Sea, whereas significantly decreasing trends are observed in the open parts of the Mediterranean Sea.

Black Sea

Of the Black Sea countries only Romania submitted chlorophyll-a data to EEA in 2008. The highest values (over 30 µg/l) were measured in the River Danube delta. Satellite observations show that ocean colour intensity is significantly decreasing in a large part of the central Black Sea.




 Bravo I, Vila M, Masó M, Figueroa RI, Ramilo I . 2008. Alexandrium catenella and Alexandrium minutum blooms in the Mediterranean Sea: Toward the identification of ecological niches. Harmful algae. 7:515-522.

 Fleming-Lehtinen, V., Laamanen, M., Kuosa, H., Haahti, H., & Olsonen, R. 2008. Long-term development of inorganic nutrients and chlorophyll a in the open northern Baltic Sea. Ambio 37(2): 86-92.

 Gowen, RJ; Tett, P; Kennington, K; Mills, DK; Shammon, TM; Stewart, BM; Greenwood, N; Flanagan, C; Devlin, M; Wither, A. 2008.  The Irish Sea: Is it eutrophic? Estua-rine, Coastal and Shelf Science 76(2): 239-254.

Koukaras, K. and Nikolaidis, G. 2004. Dinophysis blooms in Greek coastal waters (Thermaikos Gulf, NW Aegean Sea). J. Plankton Research 26(4): 445-457.

McQuatters-Gollop, A., Dionysios E. Raitsos, Martin Edwards, Yaswant Pradhan, Laurence D. Mee, Samantha J. Lavender, and Martin J. Attrill, M.J.  2007. Long-term chlo-rophyll dataset reveals regime shift in North Sea phytoplankton biomass unconnected to nutrient levels Limnol. Oceanogr., 52(2), 2007, 635–648.

 OSPAR 2008. Second OSPAR Integrated Report on the Eutrophication Status of the OSPAR Maritime Area. OSPAR Commission 2008.

 Smayda, T. 2006. Harmful algal bloom communities in Scottish coastal waters: Relationship to fish farming and regional comparisons – a review. Paper 2006/3.

 UNEP 2007. Approaches to the assessment of eutrophication in Mediterranean coastal waters (First draft). Mediterranean Action Plan. Review Meeting of MED POL Monitoring Activities and the use of indicators Athens, 12-14 December 2007. UNEP(DEPI)/MED WG.321/Inf.6 3 December 2007

 Vahtera, E; Conley, DJ; Gustafsson, BG; Kuosa, H; Pitkaenen, H; Savchuk, OP; Tamminen, T; Viitasalo, M; Voss, M; Wasmund, N; Wulff, F. Internal Ecosystem Feedbacks Enhance Nitrogen-fixing Cyanobacteria Blooms and Complicate Management in the Baltic Sea. Ambio Vol. 36, no. 2, pp. 186-194.


Supporting information

Indicator definition

The indicator shows 1) annual mean summer surface concentrations (microgram/l), 2) classification of concentration levels (i.e. low, moderate, high) and 3) trends in mean summer surface concentrations of chlorophyll-a (microgram/l) in the regional seas of Europe.

Summer period is:

  • June to September for stations north of latitude 59 degrees in the Baltic Sea (Gulf of Bothnia and Gulf of Finland) 
  • May to September for all other stations 

The used regional and subregional seas of Europe are in line with the geographical regions and sub-regions specified in the Marine Strategy Framework Directive (MSFD).  Other European Seas (Icelandic Sea, The Norwegian Sea, the Barents Sea and the White Sea) are not covered in this indicator due to current lack of data.


The concentration of chlorophyll-a is expressed as microgram /l in the uppermost 10 m of the water column during summer.


Policy context and targets

Context description

There are a number of EU Directives aimed at reducing the loads and impacts of nutrients. These include: the Nitrates Directive (91/676/EEC) aimed at reducing nitrate pollution from agricultural land; the Urban Waste Water Treatment Directive (91/271/EEC) aimed at reducing pollution from sewage treatment works and certain industries; the Integrated Pollution Prevention and Control Directive (96/61/EEC) aimed at controlling and preventing pollution of water from industry; and the Water Framework Directive (2000/60/EC) which requires the achievement of good ecological status or good ecological potential of transitional and coastal waters across the EU by 2015 and the Marine Strategy Framework Directive (2008/56/EC) which  requires the acheivement or maintenance of good environmental status in European sea basins by the year 2020 at the latest, through the adoption of plans of action based on 11 qualitative descriptors, one of which is Eutrophication.

Measures also arise from a number of other international initiatives and policies including: the UN Global Programme of Action for the Protection of the Marine environment against Land-based Activities; the Mediterranean Action Plan (MAP) 1975; the Helsinki Convention 1992 (HELCOM) on the Protection of the Marine Environment of the Baltic Sea Area; OSPAR Convention 1998 for the Protection of the Marine Environment of the North East Atlantic; and the Black Sea Environmental Programme (BSEP).


Natural and background concentrations of chlorophyll vary between regional seas, between sub-areas within the same regional sea, and between different water bodies types within a sub-area depending on physical and biological factors, such as natural nutrient loads, water residence time and annual biological cycling.

The most pertinent target with regard to chlorophyll concentrations arises from the Water Framework Directive. Target chlorophyll concentrations/ranges that support the biological quality elements at a good status (high-good boundary and good-moderate boundary) have been defined in the Commission Decision (2008/915/EC) based on the results of the intercalibration exercise carried out by the geographical intercalibration groups in Baltic Sea, North East Atlantic and Mediterranean. These target chlorophyll concentrations/ranges are determined locally for different water types and water categories, including coastal and transitional water bodies.

Chlorophyll concentration in the water column is considered as an indicator of the direct effect of nutrient enrichment in marine waters under Marine Strategy Framework Directive’s Good Environmental Status Descriptor 5: Human-Induced Eutrophication. The assessment of eutrophication in marine waters needs to take into account the assessment for coastal and transitional waters under the Water Framework Directive and related guidance, in a way which ensures comparability, taking also into consideration the information and knowledge gathered and approaches developed in the framework of regional sea conventions. Chlorophyll targets or thresholds for achieving good environmental status in marine water have not yet been determined.

Related policy documents



Methodology for indicator calculation

Methodology for indicator calculation (including description of data used)

The data used in this indicator is part of the WISE - State of the Environment (SoE) data, available in Waterbase - TCM (Transitional, Coastal and Marine) waters. Waterbase is the generic name given to EEA´s database on status, quality and quantity of Europe´s water resources. Waterbase – TCM waters contains data collected both from EEA member countries (i.e. belonging to the EIONET) and from the Regional Seas Conventions through the WISE-SoE TCM data collection process (WISE-SoE was formerly known as Eionet-Water and Eurowaternet). The resulting WISE SoE TCM dataset is therefore made of sub-samples of national data assembled for the purpose of providing comparable indicators of state and impact of transitional, coastal and marine waters () on a Europe-wide scale.

Annual mean summer surface concentrations of Chl-a, and classification of concentration levels

The primary aggregation consists of:

  1. Identifying stations and assigning them to countries and sea regions (in line with the geographical regions specified in the MSFD) 
  2. Creating statistical estimates for each combination of station and year and deriving the average annual mean summer surface concentration of Chl-a
  3. Classifying Chl-a concentration levels for each station (i.e. according to low, moderate, and high boundaries)

1. Identifying stations and assigning them to countries and sea regions

All geographical positions defined in the data are assigned to a sea region by coordinates. The used regional and subregional seas of Europe are in line with the geographical regions and sub-regions specified in the Marine Strategy Framework Directive (MSFD) (see below). Other European Seas (Icelandic Sea, The Norwegian Sea, the Barents Sea and the White Sea) are not covered by this indicator due to current lack of data. Also, because of the limited amount of data, only the following (sub)regions are distinguished in the maps: Baltic Sea, Celtic Seas, Greater North Sea, Bay of Biscay and Iberian coast, Mediterranean Sea, Black Sea.

Regional SeaSubregional Sea
Baltic Sea None

North East Atlantic Ocean

Greater North Sea

Celtic Seas

Bay of Biscay and the Iberian coast

Macaronesian region

Mediterranean Sea

Western Mediterranean Sea

Adriatic Sea

Ionian Sea and Central Mediterranean

Aegan - Levantine Sea

Black Sea none

The stations are then further classified as coastal or off-shore (>20 km from coast) by checking them against the coastal contour. Off-shore stations – open seas -  are distinguished per sub-regional sea, whereas coastal stations are further attributed to country. These classifications are done in ArcView. Smaller regions within the regional and sub-regional seas described above are used in the aggregation process of different determinants. 

EIONET stations

WISE SoE TCM data reported directly from countries are assigned to station identifiers (i.e. EIONET stations) that are listed with coordinates. For these data, which are mostly along the coast of the reporting country, stations are kept as defined.

Regional Seas Conventions data 

For the data reported the Regional Sea Conventions (and assembled by ICES), there are no consistent station identifiers available in the reported data, only geographical positions (latitude/longitude). The reported coordinates for what is intended to be the same station may vary between visits, because the exact achieved position is recorded, not the target position. Identifying station on exact position may therefore fragment time series too much.
Furthermore, duplicates between Eionet and RSC data may occur for coastal stations. A visual inspection of coastal data (< 20 km from shoreline) is therefore needed to eliminate these duplicates.

For the open waters (>20 km from shoreline), coordinates are rounded to 2 decimals, and this is used to create stations (i.e. for the purpose of establishing time series) with station names derived from rounded coordinates. As coordinates for the stations are used averages over visits to the station, rather than the rounded coordinates. This ensures that in cases were most observations are in a tight cluster within the rounding area, a position within the cluster is used. The open water observations are not assigned to countries, but listed as belonging to 'Open waters' in the Country column, without reference to country.

For the coastal ICES stations, there may be overlap with Eionet stations, and for the stations close to the coast, rounding coordinates to 2. decimal may be too much (about 500 m to 1 km). However, in this update, the rounding is done also for coastal stations, but the grouping of observations to rounded coordinates is done only within observations from each country separately, and the originator country is listed. Note that these stations are not necessarily close to the coast of the originator country.

2. Annual concentration of Chl-a per station
The statistical aggregation for calculating annual concentrations for Chl-a is done in two- or three-stage query sequences, which include:
  • Selecting season (month) and depth 
  • If needed, building a cross-table with determinants in columns, and water samples in rows, and deriving composite determinants from that. 
  • Aggregating over depth for each combination of station and date. 
  • Aggregating over dates within each combination of station and year. 

The basic data consists of two tables:

Measurements values table
WaterbaseID (Country and Station)
Date (Year, Month and Day)
Determinant with the Determinant code "Chlorophyll"

Stations table
Unique identifier: data provider, Country and StationID
Sea region (Atlantic, North Sea, Baltic, Mediterranean and the Black Sea

The two tables are combined in a query which joins data to stations, linked by WaterbaseID, and including Country Code and Sea Region (used in Selection Criteria below). This query (or a table made from it) is used in the Aggregate queries.

Description of specific aggregation query sequencesChlorophyll

Step 1

Select query selecting data for determinand "Chlorophyll-a", and including Sea Region, WaterbaseID, date and SamplingDepth.

Include data for:

  • Depth less than or equal to 10 metres and
  • Month = 6,7,8,9 (Jun.-Sep.) for stations north of latitude 59 degrees in the Baltic Sea (Gulf of Bothnia and Gulf of Finland)
  • Month = 5,6,7,8,9 ( May-Sep.) for all other stations

For each combination of WaterbaseID*Station*Date, calculate arithmetic mean of chlorophyll-a over depths.

Step 2

For each combination of WaterbaseID*Year, calculate the arithmetic mean over the depth averages from Step 1.

Export result to Aggregate database as table 't_Base_Metadata_Chl_a'

3. Classification of Chl-a concentration levels, for each station

For each (sub)regional sea, the observed concentrations are classified as Low, Moderate or High. Concentrations are classified as Low when they are lower than the 20-percentile value of concentrations within a (sub)region. Concentrations are classified as High when they are higher than the 80-percentile value of concentrations within a (sub)region. The classification boundaries therefore change between regional and/or sub-regional seas.

Trend analysis of Chl-a concentrations

Consistent time series are used as the basis for assessment of changes over time. The trend analyses are based on time series from 1985 onwards.  Selected stations must have at least data in the last four years of the current assessment (2007 or later), and 5 or more years in the overall assessment period (since 1985). Trend detection for each time series was done with the Mann-Kendall Statistics using a two-sided test with a significance level of 5% (Sokal & Rohlf 1995).

The Mann-Kendall method is a non-parametric test suggested by Mann (1945) and has been extensively used for environmental time series (Helsel and Hirsch, 2002; Hipel and McLeod, 2005). Mann-Kendall is a test for monotonic trend in a time series y(x), which in this analysis is chlorophyll concentration (y) as a function of year (x). The test is based on Kendall's rank correlation, which measures the strength of monotonic association between the vectors x and y. In the case of no ties in the x and y variables, Kendall's rank correlation coefficient, tau, may be expressed as tau=S/D where S = sum {i<j} (sign(x[j]-x[i])*sign(y[j]-y[i])) and D = n(n-1)/2. S is called the score and D, the denominator, is the maximum possible value of S. The p-value of tau is computed by an algorithm given by Best and Gipps (1974). The tests reported here are two-sided (testing for both increasing and decreasing trends). Data series with p-value < 0.05 are reported as significantly increasing or decreasing. The test analyzes only the direction and significance of the change, not the size of the change.

Methodology for gap filling


Methodology references



Methodology uncertainty

The Mann-Kendall test for the detection of trends is a robust and accepted approach. However, due to the multiple trend analyses, approximately 5% of the tests conducted will turn out significant if in fact there is no trend. Also, the accuracy at the regional level is largely influenced by the number of stations for which data is available.

There are also a number of uncertainties related to temporal and spatial use of the data. Currently two growing seasons are distinguished, one for the northern part of the Baltic Sea (June- September) and one for the southern part of the Baltic Sea, the North Sea, NE Atlantic waters, Mediterranean and Black Sea (May-September). It is questionable whether using one growing season for all waters that range geographically from the Mediterranean and the Black Sea to the North Sea and Baltic Sea, is appropriate. Moreover, currently only surface concentrations are considered. However, in the Black Sea, not only do the chlorophyll concentrations show peaks in late winter, late spring and autumn, these peaks do not only occur at the surface but also in subsurface layer (BS SoE, 2008). 

Data sets uncertainty

Data for this assessment are still scarce considering the large spatial and temporal variations inherent in European transitional, coastal and marine waters. Long stretches of European coastal waters are not covered by the analysis due to lack of data. Trend analyses are only consistent for the eastern North Sea, the Baltic Sea area and French and Croatian coastal waters in the Mediterranean.

For the assessment of chlorophyll-a concentrations, different analytical methods are generally used. Although these different analytical methods generally give comparable results with reasonable to good correlations between methods, simple fluorometric and photometric methods are less accurate and therefore may be a source of uncertainty.

Low sampling frequencies increase the risk of not detecting phytoplankton blooms, and differences in sampling frequency between stations are an additional source of uncertainty.

Rationale uncertainty

Due to variations in freshwater run-off and hydro-geographic variability of the coastal zone and internal cycling processes, trends in chlorophyll-a concentrations as such can not be directly related to measures taken, but must be evaluated in a broader context.

Data sources

Other info

DPSIR: State
Typology: Descriptive indicator (Type A - What is happening to the environment and to humans?)
Indicator codes
  • CSI 023
Frequency of updates
Updates are scheduled once per year
EEA Contact Info


Geographic coverage

Temporal coverage