Indicator Assessment

Chlorophyll in transitional, coastal and marine waters

Indicator Assessment
Prod-ID: IND-18-en
  Also known as: CSI 023
Published 29 Jan 2009 Last modified 11 May 2021
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The highest summer chlorophyll-a concentrations were observed in coastal areas and estuaries and are at many locations associated with nutrient inputs from major rivers. Of the 413 stations reported to the EEA in 2005 with more than 5 years of observations, decreasing trends in summer chlorophyll-a concentrations were found at 7% of stations, increasing trends were found at 8% of stations, and the majority of stations (85%) indicate no statistically significant change in concentration. The stations with descreasing trends are located either in the Baltic Sea or along the coast of Italy.

Map of summer chlorophyll-a concentrations observed in 2005

Note: The low category refers to values within the lowest 20th percentile and the high category refers to values within the upper 20th percentile of concentrations in a regional sea

Data source:


NE Atlantic

It is not possible to make an assessment of summer chlorophyll-a in the NE Atlantic, because data for the year 2005 only includes observations from the Seine, Brest, Loire and Gironde River estuaries, France and observations from two Scottish stations (Figure 1). In the Seine, Loire and Gironde Estuaries, average summer chlorophyll-a concentrations exceed 6.6 g/l, and they were among the highest reported to the EEA in 2005 for all of the regional seas. All time series from the region are less than five years of duration and thus trend detection is not possible based on the information available.

North Sea

In the North Sea, the highest summer chlorophyll-a concentrations in 2005 were observed at the Danish North Sea stations, Belgian coastal stations and in the Scheldt Estuary. All three locations are impacted by water from large rivers (the Danish North Sea stations are impacted by water from the Elbe River, the Belgian stations by the River Scheldt, and possibly the River Rhine) and the high summer chlorophyll-a  concentrations in the sea are likely to reflect the high nutrient loads coming from the rivers feeding into those areas (Figure 1). Observations made at at stations updated to include 2005 show that concentrations have increased at 14 % of danish stations and 7% of Swedish stations in the North Sea (corresponding to one station in each country), and increased at 14% of the danish station, but the majority of stations (91%) show no statistically significant change (Figure 2, left).  Observations made prior to 2005 suggest a smiliar pattern (Figure 2, right).

Baltic Sea

In the Baltic Sea, summer chlorophyll-a concentrations were highest at Finnish coastal stations in 2005 and in the estuaries of the rivers Vistula and Oder (Figure 1) and the concentrations at these locations were among the highest observed in Europe. Concentrations increased at 21% of the Finnish stations and 25% of Lithuanian stations (Figure 2, left),  although concentrations also decreased at 7% of the Finnish stations.  Low concentrations are predominantly observed at Baltic open water stations (Figure 1) and decreasing concentrations are found at 9% of the Danish Baltic Sea stations (Figure 2, left). In recent years the Baltic Sea has suffered from frequent and extensive summertime blooms of cyanobacteria, which are partly responsible for increasing chlorophyll concentrations.

Mediterranean Sea

The Mediterranean Sea is oligotrophic and thus summer chlorophyll-a  concentrations are lower than in the other regional seas. In 2005, the highest summer chlorophyll-a  concentrations were observed along the North East coast of Italy, in proximity of the city of Naples (Figure 1). High concentrations were also observed at single stations in Malta,and in the Gulf of Orfani in Greece (Figure 1). Only Italy and Malta has submitted long enough time series to perform a trend analysis (Figure 2 left and right) which shows that summer chlorophyll-a  concentrations are increasing at 8% of the italian stations, decreasing at 5% of the stations, and no statistically significant trend can be detected at the remaining 87% of stations.

Black Sea

No chlorophyll-a observations made in Black Sea have been subteed to the EEA. 



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


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