Lagoons are expanses of shallow coastal waters, wholly or partially separated from the sea by sandbanks or shingle, or by rocks. Salinity may vary from brackish water to hypersalinity depending on rainfall, evaporation and addition of fresh seawater from storms, temporary flooding, or tidal exchange. The distribution map is based on data submission by HELCOM contracting parties. Most of the submitted data is based on modelling and/or GIS analysis. Data coverage, accuracy and the methods in obtaining the data vary between countries.

The occurrence of suitable nursery habitats is crucial for maintaining fish populations (Sundblad et al. 2013). Species distribution modelling studies have shown the importance of suitable environmental conditions for pikeperch recruitment. Due to lack of coherent data on pikeperch spawning and nursery areas across the Baltic Sea countries, environmental variables were used in delineating potential recruitment areas for pikeperch. The pikeperch recruitment area presented on the map is mainly delineated by selecting areas where depth < 5 m, logged exposure < 5, salinity < 7 PSU, Secchi depth < 2 m and distance to deep (10m) water < 4km. The threshold values have been obtained from literature (Veneranta et al. 2011, Bergström et al. 2013, Sundblad et al. 2013, Kallasvuo et al. 2016). Temperature, although important for pikeperch, was left out due to high variation in timing of suitable spawning temperatures across the Baltic Sea. In Finnish coastal waters, a national pikeperch model (Kallasvuo et al. 2016) has been used, with very suitable areas for pikeperch generalized to 1 km grid. In Sweden, the areas delineated by environmental variables have been complemented with information from national interview survey (Gunnartz et al. 2011) as well as expert opinion.

The pressure layer represents biological pressure caused by introduction of non-indigenous species. The data is obtained from core indicator Trend in the arrival of new non-indigenous species (BSEP 129b: http://www.helcom.fi/Lists/Publications/BSEP129B.pdf). For the Baltic Sea Impact Index, the layer was normalized.

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.

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.

Distribution of Charophytes (Chara spp., Nitella spp., Nitellopsis spp., Tolypella spp.) mainly based on data submission by HELCOM contracting parties. Submitted point data was originally gathered in national mapping and monitoring campaigns, or for scientific research. Also scientific publications were used to complement the data (in Curonian, Vistula and Szczechin lagoons, see reference list). Polygon data from Poland was digitized based on Polish Marine Atlas. From Estonian waters, a predictive model was used (200m resolution), that was converted to presence/absence using minimized difference threshold (MDT) criteria. All data (points, polygon and the raster presenting predicted presence of Charophytes) were generalized to 5km x 5km grid cells.

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 “infralittoral sand” includes classes “Sand” and “Muddy sand” of the original data, in the infralittoral zone. The original polygon maps have been converted to 1 km x 1km 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.

'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.

Estuaries (according to Habitats Directive Annex I) are coastal inlets that are strongly influenced by freshwater. The distribution map is based on data submission by HELCOM contracting parties. Most of the submitted data is based on modelling, GIS analysis and/or aerial photos. Data coverage, accuracy and the methods in obtaining the data vary between countries.

This dataset contains modelled small vessel fuel consumption. This describes the geographical distribution of the fuel used by small boats. The total fuel consumption was modelled in SHEBA project to study emissions from pleasure boats. The model is based on locations and berths in marinas and leisure harbours, AIS information, statistics on fuel sale and extensive survey. For 2018 version the layer is weighted with depth, log-transformed and normalised (please see below). This dataset was also used on HOLAS 3.