Monitoring manual

The HELCOM Monitoring Manual is developed to support the implementation of the HELCOM Monitoring and Assessment Strategy and to follow-up commitments made under Baltic Sea Action Plan (BSAP) and the Marine Strategy Framework Directive (MSFD) for those Contracting Parties of HELCOM that are also EU Member States. Full background information and general introduction to the HELCOM Monitoring Manual can be found in the  introduction.

The Monitoring Manual provides information on existing monitoring programmes and their links to indicators developed to assess progress towards Good Environmental Status (GES). The information is organized along 11 main monitoring programmes or grouped according to 16 thematic programme topics. 40 sub-programmes provide the most detailed information about the monitoring. The level of regional coordination currently varies between topics while it is the ambition to develop HELCOM coordinated monitoring for all programmes.

By 2016, the Monitoring Manual will integrate existing HELCOM manuals and guidelines while at present they are still available in their current form.

In the presentation of sub-programmes there are reocurring annotations e.g. “Q5c”.  These annontations refer to specific questions required for the reporting of monitoring programmes of EU Member States under the MSFD (MSFD reporting package for Article 11).


​Monitoring programme
Programme Topic​
​Sub-programme MSFD Descriptors​
Birds Birds Marine breeding birds abundance and distribution

Marine bird health

Marine wintering birds abundance and distribution

D1, 4
Mammals Seal abundance

Health status

Harbour porpoise abundance

D1, 4
Fish Fish, shellfish and fisheries
Coastal fish

Migratory fish

Offshore fish

Commercial shellfish

 ​Fisheries bycatch

D1, 3, 4
Water column habitats ​ ​ ​ Hydrography Water column hydrological characteristics

Water column physical characteristics


D1, 5
Hydrochemistry Water column chemical characteristics


D1, 5
Phytoplankton Pigments

Species composition, abundance and biomass

D1, 4, 5
Zooplankton Species composition, abundance and biomass D1, 4
​​Seabed Habitats ​ ​ Seabed habitat distribution and extent Habitat-forming species and substrates

Seabed habitat physical characteristics​

D1, 4, 6
​Species distribution and abundance (benthic community) Hardbottom Species

Softbottom fauna

 ​Softbottom flora

D1, 4, 6
​Benthic physical loss and damage D1, 4, 6
Non-indigenous species ​Non-indigenous species ​​Non-indigenous species ​D2
​Eutrophication ​ ​ ​ ​Inputs Nutrient inputs from atmosphere

Nutrient inputs from landbased sources

Nutrient inputs from seabased sources (no info yet)

Hydrography Water column hydrological characteristics D5
Hydrochemistry Nutrients D5
Phytoplankton Pigments D5
​Hydrographic changes Hydrography Water column hydrological characteristics

Water column physical characteristics


Seabed habitat distribution and extent ​Seabed habitat physical characteristics​ ​D7
​Contaminants ​ ​ ​Inputs Contaminant inputs from atmosphere

​​Contaminant inputs from landbased sources

Acute pollution

Concentration of contaminants
​​Contaminants in water​​

Contaminants in sediment

​​Contaminants in biota

​​Biological effects of contaminants
Imposex​ D8
​​Contaminants in seafood
Contaminants in seafood​ Contaminants in seafood D9​
​Litter Litter​ Macrolitter characteristics and abundance / volume​

Microlitter particle abundance and characteristics​

Energy, including underwater noise Underwater noise​ ​Ambient noise

Registry of impulsive sounds​ (no info yet)