Guanabara Bay (GB) is the second largest bay in the coast of Brazil (384 km2) (22o41 to 22o56 S ; 43o02 to 43o18 W). In its surroundings live 16 million inhabitants (6 million in Rio de Janeiro city). This system experiences steep spatial gradient from the entrance to inner bay. GB receives high load of nutrients and organic material from riverine sources and from domestic and industrial sewage inputs. As a consequence, this system is characterized as a high eutrophicate and polluted one. In spite of its poor environmental status, GB still presents many living resources who use the bay as a refuge, feeding and nursery grounds, with some of those species having commercial interest. An important characteristic of GB is the influence of South Atlantic Central Water, a deep, cold and rich nutrient water, that enters the bay during the Cabo Frio upwelling period. This phenomenon permits to maintain the bay at a relative good health level in its central part, in contrast with the marginal areas highly polluted. Although encroached on by urban expansion, the inner east margins of Guanabara Bay is still bordered by a 90 km2 fringing mangrove system, of which 43 km2 is an environmental protection area, Guapimirim.

The Asinara Gulf covers approximately 500 km2 and is the second largest bay in Sardinia. The Gulf is limited by Asinara Island (National Park) in the west side and by Castelsardo town in the east side. The average depth of the gulf is approximately 35-40 m and only 35% of the gulf bottom has a depth exceeding 50 m. The predominant winds are from the I and IV quadrant. The marine area of the gulf has been affected since the ‘70s by different human impacts, especially by those connected to the industrial centre of Porto Torres. The main urban centre along the gulf coast is Porto Torres, with an important industrial, commercial and passenger harbour. A long-term series of data is available since 1997 and derives from high-frequency measurements and samplings to assess environmental and biological parameters. In particular the data concern the main trophic descriptors (Secchi depth, temperature, pH, conductivity, dissolved oxygen and saturation, alkalinity, NH4-N, NO2-N, NO3-N, total nitrogen, soluble reactive phosphorus, total phosphorus, dissolved silica) and phytoplankton abundances, as chlorophyll a, cell densities and biomass, class and species composition. Data collection started in 1997 and continued, with few gaps of various sizes of time, up to 2007. The data collection resumed in 2007 only seasonally.

Patos Lagoon is the largest (1,036,000 ha) choked lagoon in the world, extending from the city of Porto Alegre (30º30’ S) to Rio Grande (32º12’ S) in southern Brazil, at the Atlantic coast of South America. In the southern reaches, the Patos Lagoon Estuary and Adjacent Coast (PLEA) present high biological productivity and at the same time provide significant ecosystem services including artisanal and industrial fisheries, an industrial conglomerate and is home to an important maritime port. The hydrology and biology of the ecosystem has been studied since the nineteenth century and the site has been included in the framework of the Brazilian Long Term Ecological Research in 1998. Systematic analysis has been conducted of abiotic and biotic information unraveling the functioning of the ecosystem and their organisms from phytoplankton to marine mammals. Climatic events and human activities both affect the ecology of the highly dynamic PLEA. This shallow warm temperate estuary is river dominated, and freshwater discharge peaks are strongly associated with El Niño Southern Oscillation - ENSO episodes. Rainfall increases significantly during El Niño periods, while low discharge occurs during La Niña when drought conditions are observed. These phenomena influence salinity, physico-chemical water characteristics and sediment dynamics in the estuary, which in turn influence the biota. Long-term continuous studies (more than 25 years) have demonstrated that significant changes of phytoplankton, zooplankton, macrobenthic fauna and flora, crustaceans, fish and marine mammals in these coastal ecosystems are induced by natural impacts and human-related factors. Moreover, freshwater water discharge to the Atlantic Ocean has an overriding influence on ecological processes in the adjacent coastal region and vice-versa fishing activities on the coastal region influence the ecology of the estuary. These conclusions were only possible due to long-term continuous studies conducted in the Patos Lagoon estuary and adjacent coastal region, making this dataset the most comprehensive in South America.

The site is divided into two different types of environments: 1. Coastal marine environments. Marine coastal areas of Sardinia, in particular, the Gulf of Asinara in the north and the Gulf of Olbia in the north-east, affected by different types and intensities of human impact and by the resulting presence of different environmental conditions from the point of view of water quality. 2. Lagoons and coastal ponds. Lagoons and coastal ponds located along the west-central coast of Sardinia, in the Gulf of Oristano. These sites are all important wetlands included in the Ramsar Convention, are IBA (Important Birds Area) and SIC and ZPS. The ownership of the sites is the Regional Government of Sardinia. Fisheries and aquaculture are generally the most important human activities, and there are also educational and recreational activities. They are affected by various environmental issues, mostly related to the process eutrophic.

The Slapy reservoir is a part of the Vltava Cascade, a system of nine reservoirs together retaining 1.4 billion m3 of water. The dam of the Slapy reservoir was constructed at the 91.7 km of the Vltava River in 1949–1954 and the reservoir impounded in 1955. The dam is 60 m high and 260 m long. Reservoir volume is 270×106 m3. Just below the Slapy dam, there is the end of impoundment of the small Štěchovice reservoir (built earlier in 1938–1944). Only several small brooks enter the impoundment of the Slapy reservoir, the mean yearly flow through the Slapy reservoir is 83.8 m3 s-1 and the mean hydraulic retention time is 38.5 days. A large Lipno reservoir in the upper part of the Vltava River was built in 1952–1959. In 1961, another part of the Vltava Cascade, large Orlík reservoir was built above the Slapy reservoir and later several small reservoirs. The total catchment area of the Slapy reservoir is 12 968 km2. The Slapy reservoir is a canyon shaped water body mostly with steep banks. An electric power station, working in peak hours (morning and evening), is located in the dam. As a consequence, periodic seiches occurred, water level fluctuates, and a littoral zone with aquatic plants is not developed. The reservoir is intensely used for recreation and locally as a drinking water source. Regular investigations include major physical and chemical characteristics and pelagic biota (bacteria, protists, phytoplankton and zooplankton). The sampling point is located 8.8 km downstream of the dam in a lacustrine zone of the reservoir. Long-term research in the reservoir already yielded valuable results explaining long-term effects of anthropogenic and land use changes in the catchment, such as the construction of the upstream reservoir, agricultural practice (e.g. drainage, changes in arable land area and fertilization rate), wastewater treatment, road de-icing etc., on water chemistry and biology.

The separation line of the semi-enclosed northern basin from the rest of the Adriatic Sea is conventionally defined at the 100 m isobath, at about 43°20’N, from where the bottom depth moderately decreases up to the northern coast reaching the smallest average depth in the northernmost protrusion of the basin, the Gulf of Trieste (surface area 600 km2, volume 9.5 km3, maximal depth approx. 25 m). The oceanographic properties of Gulf of Trieste are affected by water mass exchange with the northern Adriatic at the open western boundary, by local meteorological conditions that induce a pronounced seasonal cycle of seawater temperature (6 - 28 oC) and by the largest freshwater input, the Soča (Isonzo) River. The latter enters the Gulf on the shallower northern coastline with an average flow of 123 m3 s-1 and represents the major source of land-borne nutrients in this coastal zone, in particular of nitrate, whereas inputs along the south-eastern coast are comparatively small (contributing less than 10% to the freshwater balance in the Gulf). The circulation pattern is variable, however the prevailing ENE wind is the most efficient for the water exchange, especially during winter. These physical features, in addition to freshwater inputs, are ultimately reflected in the distribution of nutrients and in the seasonal and inter-annual variability of plankton communities, primary production but also in events of hypoxia/anoxia and mucous macroaggregates, which have characterised the whole northern Adriatic basin in the recent past. The waters of the Gulf of Trieste have been monitored for several physical-chemical and biological variables since 70s’ but the longest and most continuous data set of biological variables is represented by the phytoplankton time series, which started in 1990 when the national monitoring programme has become operational (set by Slovenian Environmental Agency). From 2007 onwards, the monitoring programme complies with the regulations of the EU Water Framework Directive (2000/60/EC).

The site is situated in lowlands of Central Poland and arranged around the Sulejowki Reservoir. It has been build in 1969-1974 on the Pilica River mainly as a source of drinking water for the City of Lodz (the third biggest city in Poland) and other cities like Tomaszow, Piotrkow, Sulejow, and a power generator. With time it became also an important touristic and recreational place. The research area includes the reservoir and its direct catchment, where smaller plots have been located for analysing surface flow, groundwaters, and the role of land/water ecotones in regulation of nutrient cycling. There is number of sampling sites/points located also on the reservoir, 3 of them are permanent since 1980's and serve as a source of data on water chemistry, the others are sampled periodically for certain purposes, e.g. fish (including 1+), phytoplankton, zooplankton, sediment depositon, groundwater level, groundwater chemistry.

The Gulf of Naples has an extension of ca 870 kmq and an average depth of 170 m. The coastal area, which is inhabited since pre-Roman age, is densely populated and small factories are actively growing. In the Gulf, polluted areas (Sarno river mouth, harbours) coexist with pristine areas, including some Protected Marine Areas. Research on marine organisms has started before since the beginning of 1800, but first ecological studies date back to the 70ies of the last century. The long-term monitoring station (LTER-MC, 40°49’N, 14°15’E) is located 2 nm off Naples city (depth ca 75 m) at the boundary between eutrophied coastal waters and oligotrophic Tyrrhenian waters. Larger areas of the Gulf have been sampled occasionally in several cruises. The MC data set represents one of the few plankton time series available in the Mediterranean Sea, and it is certainly one of the longest.

Black Sea site includes three areas: cape Kaliakra, cape Galata and Varna Bay, and Koketrays Sand bank (only for macrozoobenthos). They were chosen on the base of historical data availability and eutrophication/pollution impact. Kaliakra marine area is influenced by eutrophication due to mainly the Danube river inflow. The local anthropogenic impact in the region is insignificant. It is a nature reserve. Cape Galata and Varna Bay sites are under the indirect impact of Varna Bay current and the system Beloslav lake-Varna lake - a cascade introducing nutrients and pollutants of industrial (chemical industry), agricultural, sewage origin and nearby ports. Koketrays Sand bank is an unique benthic habitat. The coordinates of the selected areas are as follow: c. Kaliakra: 28.416667 43.366667 c. Galata: 27.933889 43.186111 Varna Bay: 28.166667 43.166667 Koketrays bank: 27.888889 42.635556

The Darss-Zingster Bodden is a tideless flat brackish inner coastal water of the Southern Baltic Sea. It consists of 4 consecutive water basins connected by narrow streams. This forms a gradient of salinity from 1-14 PSU and a eutrophication gradient.