Input of impulsive anthropogenic sound includes impulsive events from 2011-2016 • Seismic surveys (HELCOM-OSPAR Registry; national data call submissions as lines in the folder of data) • Explosions (HELCOM-OSPAR Registry) • Pile driving (HELCOM-OSPAR Registry) • Airguns (HELCOM-OSPAR Registry) For the different event types, numeric intensity value was used to represent the pressure as categorized in HELCOM-OSPAR Impulsive noise registry. All nationally reported seismic surveys were given intensity values “Very low” (0.25) - Very low (0.25) - Low (0.5) - Medium (0.75) - High (1) The impact distance has not been taken into account due to the different nature of separate datasets used for the pressure layer. We acknowledge that e.g. pile driving and airguns may impact up to 20 km from the source event. The spread of the sound wave depends on the sound frequency, water salinity, temperature and density.

Baltic International Trawl Survey (BITS) data (2011-2016) from ICES DATRAS database was used as a base to create a map of cod relative abundance (quarter 1 data, CPUE values per ICES subdivision). Cod = 30cm was included. For ICES rectangles surveyed by BITS, values shown are the mean CPUE per ICES subdivision based on BITS data, average for 2011-2016. For ICES rectangles not surveyed by BITS, values are calculated as: MAX-value x Weighting factor. The weighting factor is specific to each ICES rectangle, calculated as the ratio between the commercial landings in that rectangle and the commercial landings in the ICES rectangle with highest landings (based on averages for 2011-2016). MAX-value = CPUE according to BITS in the ICES rectangle with highest landings. ICES rectangles outside the BITS survey area with no reported cod landings were given the value 0. Values were first log transformed and then normalized.

Broad-scale habitat maps for the Baltic Sea have been produced in the EUSeaMap project in 2016. For German and Estonian marine areas, national (more accurate) datasets were used. German data included both substrate and light information (division into infralittoral/circalittoral). Estonian data included only substrate and the division into light regimes was obtained from the EuSeaMap data. Here, the habitat class “circalittoral mixed substrate” includes classes “mixed sediment” of the original data, in the circalittoral zone. The original polygon maps have been converted to 1 km x 1 km grid. The scale of the substrate data used in broad-scale habitat maps varies from 1:250 000 to 1:1M (data from EMODnet Geology). Coarser resolution data has been used in areas, where 1: 250 000 substrate data has not been available. Due to different scales used, the habitat classes may show different sized patterns in different areas.

Esker islands (according to Habitats Directive Annex I) are glaciofluvial islands consisting mainly of relatively well sorted sand, gravel or less commonly of till. Also their underwater parts are included in the habitat. The distribution map is based on data submission by HELCOM contracting parties. Only Sweden and Finland reported occurrences of esker islands. Only underwater parts are included in the datasets. The data is based on modelling and GIS analysis. Data coverage, accuracy and the methods in obtaining the data vary between countries.

Distribution of Furcellaria lumbricalis based on data submission by HELCOM contracting parties. Mainly pointwise occurrences of Furcellaria were submitted, originally gathered in national mapping and monitoring campaigns, or for scientific research purposes. From Estonian waters, a predictive model was used (200m resolution), that was converted to presence/absence using minimized difference threshold (MDT) criteria. For Poland, only confirmed occurrence of Furcellaria were included (Slupsk bansk, Rowy reef and reef at Orlowo cliff). All data (Furcellaria points and the raster presenting predicted presence of Furcellaria) were generalized to 5km x 5km grid cells.

'Availability of deep water habitat, based on occurrence of H2S' layer describes the suitability of the bottom areas for the Baltic Sea biota, with regard to oxygen conditions of the near bottom waters. The data used to produce the layer was received from Leibniz-Institut für Ostseeforschung Warnemünde (IOW): - areas (polygons) with hydrogen sulfide (H2S) based on point measurements and modelling. Five time periods / year, for years 2011-2016 (altogether 30 layers). The polygons were converted to raster layers in a way, that for each time period (6 years, 5 time periods each year), areas with H2S got a value 0, other areas got the value 1. All layers were summed, (representing 6 years, 5 time periods each year, maximum value 30) and data was normalised. For more detailed information on the data used, please see Feistel et al. 2016.

Input of heat pressure dataset contains delta heat values from warm water discharge of - Discharge of warm water from nuclear power plants - Fossil fuel energy production. The Discharge of warm water from nuclear power plants was requested from HELCOM Contracting Parties. Average temperature change of the cooling water (°C) and amount of cooling water (m3) was used to calculate the heat load in TWh. No data on heat load was available for the Leningrad nuclear power plant; therefore the average heat load (TWh) of discharge of warm water from nuclear power plants was given. No heat load information was available for fossil fuel energy production sites. Heat load of 1 (TWh) was given to all production sites, based on average heat load of individual production site in Helsinki from recent years. 1 km buffer was used for both datasets with steep decline around the outlet. Overlapping areas were summed. Heat load from both layers were summed and the layer was normalized.

Input of hazardous substances pressure layer is interpolated from CHASE Assessment tool concentration component. The contamination ratio values were calculated with CHASE Assessment tool for hazardous substances monitored in water, sediment and biota. Classified mean contamination ratio was used in the interpolation. Classification is based on the http://stateofthebalticsea.helcom.fi/about-helcom-and-the-assessment/downloads-and-data/. The points were interpolated to cover the entire Baltic Sea with Spline with barriers interpolation method. Please see "lineage" section below for further details on attributes, data source, data processing, etc.

Boreal Baltic islets and small islands (according to Habitats Directive Annex I) are groups of skerries, islets or single small islands, mainly in the outer archipelago or offshore areas. They are important nesting sites for birds and resting sites for seals. The surrounding sublittoral vegetation is also included. The distribution map is based on data submission by HELCOM contracting parties. Only Sweden and Finland reported occurrences of boreal Baltic islets and small islands.

This map presents the Special Protection Areas (SPAs) with reported wintering areas for birds. The spatial data on SPAs were gathered from the HELCOM contracting parties by Lund University, Sweden. In the data, the countries also indicated whether the sites were designated mainly due to wintering or breeding birds in the area. For Denmark, the information was obtained from standard forms for Natura 2000 sites. For Denmark, the data was updated after review process 20 February 2017. For Germany, the areas that were reported as “NA”(=information not available) were included in both breeding and wintering area maps. Many of the SPAs are both wintering and breeding areas. For the Baltic Sea Impact Index, the data was converted to 1 km x 1km grid cells.