This is a long-term monitoring study of freshwater zooplankton and phytoplankton population changes after introduction of the mysid, Mysis relicta Lovén, 1862 in lake Jonsvatnet. It is an oligotrophic lake located in central Norway (63° 22’ N, 10° 37* E), 150 m above sea level. The lake has three basins divided by narrow sounds with depths of 1 – 3 m. The major basin is Store Jonsvatnet with surface area of 12,4 km2 and the two smaller ones are Lille Jonsvatnet and Kilvatnet with surface areas of 1,6 km2 and 0,8 km2 respectively. The maximum depths of the three basins are 97 m, 37 m and 34 m respectively and the average depth of the lake is 37 m. Method: Plankton are sampled at one station in each lake basin. All samples are taken during the period June-October, twice a month in June - August, once a month in September and one sampling of mysids in late October. Zooplankton is sampled with a 1 m long tube sampler (volume 5 l). A vertical column of water extending from 0 to 20 m depth is consistently sampled every 1 m. Samples from 5 m layers are mixed together and treated as one sample. Phytoplankton is sampled with a water sampler (volume 1.6 l). A vertical column of water extending from 0 to 10 m depth is consistently sampled every 1 m. Samples from 5 m layers are mixed together and treated as one sample. Mysis relicta is sampled in Lille Jonsvatnet with vertical net hauls (net opening 1 m2, mesh size 500 µm) from 1 m above bottom to to the surface.

Lake Candia is a small and shallow lake, located in North-Westerm Italy. The mean elevation is 226 m a.s.l., the surface is 1,5 km², the max depth 7,7 m, the mean depth 4,7 m and the volume 0,007 km3. Lake Candia has suffered during its evolution a natural increase of its trophic state, undergoing a process of eutrophication culminated with a marked worsening of his ecological quality since the '60s. In the late '70s and mid '80s, this ecosystem was affected by fish mortality episodes and by the enormous development of emerged and submerged aquatic macrophytes. The systematic scientific study of Lake Candia began in 1985, when the CNR of Verbania was asked to perform a limnological research with the aim to propose a possible restoration intervention. In addition to the control of pollution sources from the basin, environmentally sound technologies were applied to reduce the effects of eutrophication, such as biomanipulation of the aquatic food chain and macrophyte control and management.The experiment conducted in Lake Candia has shown that significant improvements can be achieved through the management of a specific key components of the biocenosis of the lake. Data collection activities on hydrochemistry, phytoplankton, zooplankton, fish fauna, macrophytes, as well as physical limnology, took place from 1986 until 2012. To date, only hydrometeorological data collection (precipitation, air temperature, wind, solar radiation and lake levels), started in 1987, is active. LTER specific topics are: Long-term analysis of changes in community functional diversity of phyto-and zooplankton. Evaluation of the lake ecosystem response to short and intense rainfall events, in relation to the increase of nutrients input through runoff.

The Neusiedler See - Seewinkel National Park is the first cross-border National Park in Austria and the first Austrian National Park recognised by the IUCN. It covers in total about 90km² on Austrian territory. About 50% of the area (about 4500 ha) is a Nature Reserve Zone, which remains untouched by humans. This zone is dominated by the southernmost Austrian part of the reed belt from Lake Neusiedl. The Conservation Zones are mainly cultural landscapes and require landscape conservation measures and habitat management like pasturing, mowing, cutting reed or water retention. These measures are taken to preserve the cultural landscape and its biodiversity that has developed over centuries. Important habitats like 160 km² of reed belt and around 40 periodically dry soda lakes, as well as sand habitats, dry and wet meadows can be found closely associated with vineyards, cropland, touristic infrastructure and rural settlements. Long-term monitoring programs regarding bird populations, fish ecology or the grazing management enable the cross-border National Park Neusiedler See - Seewinkel to provide biological data from flora and fauna. Furthermore, all soda lakes are monitored frequently regarding salinity, oxygen, temperature, color etc. and biological parameters such as species diversity and quantity of macrozoobenthos. Due to the mosaique of protected and non-protected areas, the boundaries of the National Park area are difficult to define on the shown map.

Lake Stechlin is a a deep clear-water lake located in a nature reserve approximately 80 km north of Berlin, Germany (53°10°N, 13°02° E), at 59 m elevation.The lake basin was formed during the last continental glaciation some 12,000 years ago and today is situated at the transition between temperate/maritime and temperate-continental climates.The drainage basin is almost completely covered by forest (95%), with the exception of the area of a former nuclear power plant and a small village, which diverts its wastewater into a different drainage basin. The shoreline of Lake Stechlin is largely undeveloped with no notable infrastructure. The seepage lake is essentially fed by precipitation and groundwater, resulting in a theoretical water retention time of greater than 40 years.

The Gulf of Venice is a gulf that borders modern-day Italy, Slovenia and Croatia, and is at the north of the Adriatic Sea between the delta of the Po river in northern Italy and the Istria peninsula in Croatia. The site is under a heavy antropic impact (nutrient loads, coastal towns, fishery, tourism maritime routes). In the past eutrophic events struck the ecosystem and, more recently, frequent mucus macro-aggregates extended in the whole basin. Study of long term historical time series of the biotic community in the Gulf of Venice in relation with the biogeochemical cycles and physical properties of sea-water have been conducted since the '70s.

The Elbe River is one of the major rivers in Central Europe. It springs at an altitude of about 1,400 meters in the Giant Mountains in the north of the Czech Republic. It flows through eastern, middle, and northern Bohemia, and its catchment area includes most of Bohemia. The Elbe traverses the northeastern part of Germany and flows into the North Sea. The total river length is 1,094 km. In the Czech Republic, the monitored river length is 371 km and the catchment area includes 49,933 km2. The average flow at the Czech-German borders is 311 m3 s-1. Many weirs dam the watercourse of Elbe River in the Czech Republic. This artificial intervention is crucial for the characteristics of the riverbed, its width, depth, and bottom substrate. The width of the riverbed in the monitored area ranges from approx. 10 m on the upper course to approx. 150 m on the lower course and river sections above the weirs. The depth of the river varies from 0.5 m in the upper parts and below the weirs to more than 5 m in the lower course and above the weirs. The bottom substrate varies from the stony, gravelly, and sandy fractions in shallow and fast-running sections to muddy/silty fractions in slow-running sections above the weirs. The main tributaries of the Elbe in Bohemia are Metuje, Orlice, Jizera, Ploučnice, Vltava, Ohře and Bílina rivers. The catchment area is densely populated. The river is exposed to various sources of pollution (organic, agricultural, and industrial) and hydromorphological pressures (straightening, shortening, regulation of meanders, and fragmentation of river continuity). There are seven permanent monitoring sites on the Elbe River in the Czech Republic: Děčín (river kilometer 747.9), Litoměřice (796.9), Obříství (842.1), Lysá nad Labem (878.8), Valy (954.7), Hradec Králové (994.4) and Vestřev (1051). The Elbe basin long term environmental research has been organised by the Ministry of Environment of the Czech Republic and cooperation institutions since 1993. More than 600 physicochemical parameters, including sensory properties of water, are regularly monitored in at least nine different types of matrices (water, sediment, periphyton, floats, sedimentable floats, benthos, fish tissues, fish fry, and Dreissena polymorpha tissue) and using passive samplers. Among the main monitored characteristics belong balances of macroelements (carbon, nitrogen, oxygen, phosphorus), concentrations of inorganic salts, heavy metals and various organic pollutants such as pesticides, personal care products (including drugs) and other anthropogenic substances in the environment. Characteristics such as abundance and species composition are regularly monitored in fish, macrophytes, macrozoobenthos, phytobenthos and plankton.

Western part of the Gulf of Riga (the Baltic Sea) littoral and sublitoral zone. The marine site is located on the west coast of the Gulf, in the Engure Nature protected area. The monitoring activities are based on three transects which represent an open area of very similar substrate type. These transects are located on the tip of Mersrags, 2.5 km northwards from the port of Mersrags. Long-term studies of the Gulf of Riga coastal zone communities and macrophytes as the key component of littoral zone under natural and anthropogenic impact and possible threats to the littoral zone biological resources. The SCUBA diving is used in marine site assessment.

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

How do freshwater ecosystems react to changing environmental conditions and to what extent can these changes be captured in the dynamics of eco-evolutionary processes? The project REES ('Rhine Eco-Evolutionary System') aims at the long-term assessment of eco-evolutionary interactions in the Rhine as a limnic habitat under consideration of diverse associated water bodies. The study area includes the main flow channel of the Rhine (km 845, North Rhine-Westphalia), as well as Rhine oxbows, Rhine water-fed gravel pit lakes in ecological succession and the surrounding floodplain (Rees, district of Kleve). The Ecological Research Station Rees-Grietherbusch of the Institute of Zoology (University of Cologne) and the Nature Conservation Center District Kleve e.V. form the central infrastructure of the study area. In addition, the Ecological Rhine Station of the University under the direction of Prof. Dr. Arndt is also associated to the project, which enables direct sampling and experimental recording of the main Rhine flow channel. The extensive system of standing and flowing freshwater bodies covered in the REES study site allows the investigation of dynamic variations in biodiversity composition at all levels, from species diversity of communities to genomic diversity at the molecular level of individuals and populations. Along a selected trophic cascade, representative species will be long-term observed and analyzed ecologically and especially also (population-)genomically. The incorporation of ecological genomics is the core aspect of this LTER-D project, which is intended to capture the feedback of evolutionary changes on the ecological system. Population genomic approaches can be used to infer both evolutionary and ecological processes from genomic data. To cope with the dimension of this project, REES is designed as an interdisciplinary collaboration project and currently counts seven project partners with corresponding subordinate projects.