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Pikeperch is a major predator in the pelagic zone of eutrophic waters, such as the large north-temperate lowland lakes Vortsjarv (Estonia) and Peipsi (Estonia/Russia). The size and structure of the pikeperch population is strongly influenced by their success at the juvenile stage. Therefore, we investigated the diet and prey selection of pikeperch fry caught in the ice-free period in lakes Peipsi and Vortsjarv in 2007 and 2008. We analysed the stomach contents of 635 pikeperch from Lake Peipsi and 202 pikeperch from Lake Vortsjarv, and compared our findings with similar data from the 1950s (Erm, About Biological and Morphological Differences of Pikeperch. Hydrobiological Researches II (in Estonian), 1961). Analysing 4–20 cm long fry, we studied differences in prey size, seasonal diet patterns and the ontogenetic diet shift. In both lakes, 0+ pikeperch feed mostly on large predatory zooplankters. However, in Lake Peipsi the stomach content weight and the average number of food items in stomach were higher, and the food spectrum was wider than in Lake Vortsjarv. There was also a difference in the type of food that dominated fry’s stomach content (calculated by weight) in the two lakes. In Lake Peipsi, chironomids larvae, as well as zooplankters Daphnia galeata and Bythotrephes longimanus dominated, while in Lake Vortsjarv zooplankters Mesocyclops leuckarti and Leptodora kindti. Seasonal analysis showed that cladocerans dominated in pikeperch fry stomach content in summer and at the beginning of September, but copepods were dominant in autumn and spring. In contrast to the studies carried out from 1952 to 1958 (Erm, About Biological and Morphological Differences of Pikeperch. Hydrobiological Researches II (in Estonian), 1961), the shift from planktivory to piscivory at the end of the first growing season was hardly ever observed during our investigation. We believe this is due to the lack of suitable prey fish as there was a collapse of the smelt, Osmerus eperlanus (L.), population in both lakes. The transition of pikeperch from planktivory to piscivory was delayed till the next summer.

We analysed lake smelt (Osmerus eperlanus eperlanus m. spirinchus Pallas.) population dynamics in relation to water level and temperature in Lake Peipsi, Estonia/Russia, using commercial fishery statistics from 1931 to 2004 (excluding 1940–1945). Over this period, smelt provided the greatest catch of commercial fish although its stock and catches have gradually decreased. At times, catches of smelt were quite variable with a cyclic character. Disappearance of smelt from catches in years 1973–1975 was the result of summer fish kill. Regression analysis revealed a significant negative effect of high temperature on the abundance of smelt stock, while the effect of water level was not significant. Our results suggest that critical factors for the smelt population are the absolute value of water temperature in the hottest period (≥20°C) of summer and the duration of this period. These weather parameters have increased in synchrony with smelt decline during the last 7 decades. There appeared to be a significant negative effect of hot summers on the abundance of smelt operating with a lag of one and 2 years, which can be explained by the short life cycle (mainly 1–2 years) of this species.

Limnological monitoring data and palaeorecords from large shallow Lake Pskov were used to study the long-term dynamic pattern of the lake ecosystem and to identify the start of its degradation. Lake Pskov is the southern part of Lake Peipsi s.l., the largest transboundary lake in Europe. The limnological monitoring data collected in the years 1956–2005 show that the water quality of L. Pskov has deteriorated and caused adverse changes in the whole ecosystem (e.g. excessive growth of algae, increased cyanobacterial blooms, silting of the lake bottom, fish kills). Doubled total phosphorus (Ptot), dissolved inorganic P (PO4-P) and chlorophyll a (Chl-a) contents, increased total alkalinity (HCO3 −) and pH, as well as decline in water transparency and oxygenation conditions, indicate a clear increase in the trophic level of the lake. However, the limnological studies do not show when the degradation started. To understand long-term dynamics of the lake ecosystem, a 52 cm sediment core taken from one monitoring station of L. Pskov was studied and dated by the 210Pb method. Palaeodata show that substantial changes in the L. Pskov ecosystem started already in the 1930s when mesotrophic conditions in the lake turned increasingly eutrophic. Since that time, the content of P, nitrogen (N), carbon (C) and relative abundance (RA%) of planktonic diatoms in the sediment have increased significantly (P 0.9 or r

Ruffe is one of the most numerous fishes in Estonian large Lakes Peipsi (area 3555 km2, mean depth 7.1 m) and Vortsjarv (270 km2, 2.8 m). Owing to its small size ruffe has little value for commercial or recreational fisheries today. However, due to their high abundance, ruffe play an important role in the food webs of both lakes. The aim of the investigation was to establish the proportion of ruffe in the fish community and to assess the wellbeing of this fish in the two lakes on the basis of growth rate and condition factor. According to experimental catches made in autumn 1998–2002, the average total catch of fishes per trawl-hour (CPUE) in L. Peipsi was about two times higher than in L. Vortsjarv (204 kg and 105 kg, respectively). CPUE of ruffe made up 16 kg in L. Peipsi and 7 kg in L. Vortsjarv. In these lakes the fish community composition and food resource appear to be different. Benthivorous fishes were dominating in L. Vortsjarv and the biomass of macrozoobenthos was significantly lower in this lake than in L. Peipsi. In the first year, the growth rate of ruffe was higher in L. Peipsi where the state of zooplankton was better compared with L. Vortsjarv. Differences in the linear growth rate of older fishes in L. Peipsi and L. Vortsjarv were not significant. The lower condition factor of ruffe in L. Vortsjarv reflects the limited food resource of abundant benthivorous fishes in this lake. Different trophic relationships in Estonian large lakes are better reflected in the ruffe's condition factor than in its linear growth rate.

The stomach contents of eel, bream and ruffe were examined in order to detect the diet overlap and possible food competition between these benthophagous fishes in the eutrophic Lake Vortsjarv. The frequency of occurrence, mean number and mean restored weight of food items per individual were used for the description of their diet. Overlap in diet of bream (standard length >15 cm), eel (SL>30 cm) and ruffe (SL>4.5 cm) appeared mostly in respect of Chironomus plumosus (L.) larvae and pupae, which may lead to food competition between these fishes. However, these fishes can eat different chironomid instars. Unlike eel, who takes mainly large fourth-instar larvae and pupae of C. plumosus, ruffe and bream eat, in addition, small third-and second-instar larvae of this species as well as other small-sized chironomids, mainly Einfeldia carbonaria (Meig.), Microchironomus tener (Kieff.) and Procladius spp. Obviously, even if the overlap was pronounced, serious competitive interactions would arise only in case of limited food resources in the years with a low biomass of C. plumosus. A significant correlation (r= 0.88; P < 0.05) was found between the mean biomass of fourth-instar larvae of C. plumosus in the lake sediment and in the stomach of ruffe in different years. The diet composition of ruffe was more diverse (including a wide range of invertebrates, fish ova and detritus) than that of eel and bream. Evidently, omnivorous mode of feeding provides ruffe with an advantage over other benthophagous fishes living in the lake. Unlike eel and bream, ruffe continued to take food in late autumn and winter when water temperature in L. Vortsjary decreased to 2–0.2°C.

Lakes in Europe have a bipolar distribution by latitude with higher lake densities in the north (58–65° N) and south (38–48° N). By area, 95% of the large lakes (>100 km2) are located at altitudes lower than 100 m above sea level (ASL) and only 1% lie higher than 1,000 m ASL. Physically large lakes exhibit several similarities to seas and oceans in their thermal structure and circulation dynamics. From the chemical point of view, lakes are important accumulation sites for substances transported from the watershed or built up in the lake itself but they may contribute positively to global greenhouse gas emission. Fauna and flora of ancient large lakes such as the Caspian Sea and Lake Ohrid include large numbers of endemic species, which become endangered if conditions change because of direct human impact, alien species invasions or climate change. Large lakes offer a wide range of ecosystem services to society, the multiple use of which creates multiple pressures on these water bodies such as nutrient load and toxic pollution, modification of hydrology and shore line structure, and shifting of the food web balance by stocking or harvesting various species. Although large lakes are among the best-studied ecosystems in the world, the application to them of environmental regulations such as the European Water Framework Directive is a challenging task and requires that several natural and management aspects specific to these water bodies are adequately considered.

Data for the vegetation periods (May–November) of 1985–2003 were used to collate the nutrient content and biomass of the most important phytoplankton groups in Lake Peipsi (Estonia). Two periods differing in external nutrient load and water level were compared by analysis of variance. The years 1985–1988 were characterized by the highest loads of nitrogen and phosphorus, high water level and cool summers. The years 2000–2003 were distinguished by low or medium water levels and warm summers. The first period showed statistically significantly higher values of total nitrogen (Ntot) and a higher Ntot:Ptot mass ratio. The second period showed a higher content of total phosphorus (Ptot), a higher ratio of dissolved inorganic compounds N to P and higher phytoplankton and cyanobacterial biomasses. Comparison between parts of the lake demonstrated that the differences between the two periods were more evident in the shallower and strongly eutrophic parts, Lake Pihkva and Lake Lammijarv, than in the largest and deepest part, the moderately eutrophic Lake Peipsi s.s. Temperature and water level acted synergistically and evidently influenced phytoplankton via nutrients, promoting internal loading when the water level was low and the temperature high. The effect of water level was stronger in the shallowest part, Lake Pihkva. The difference in Ptot content between the southern and northern parts was twofold; the Ntot:Ptot mass ratio was significantly lower in the southern parts, and phytoplankton biomass (particularly the biomass of cyanobacteria) was significantly higher for Lake Pihkva and Lake Lammijarv than for Lake Peipsi s.s.

A comprehensive study (chronological, lithological and geochemical) of an 8.5 m postglacial sediment sequence from Lake Peipsi was conducted to elucidate the effects of lake-level changes on the sedimentary environment and biogeochemical dynamics in a large lake. Four lithological units were distinguished in the sediment sequence studied: clayey silt, slightly laminated greyish carbonaceous gyttja, brownish-grey gyttja and dark gyttja. These units indicate that large shifts in sedimentation processes occurred in the past. The sediment data show that fluctuations in water depth had a profound impact on the lake environment, recorded as changes in the lithological composition, phosphorus content of sediments and composition of diatom assemblages. The corresponding changes are best reflected in sediments accumulated during phases of regression when the lake area was also smaller. As the water depth and area of the lake increased, wave-induced erosion and resedimentation smoothed or even disturbed the initial information. The increase of phosphorus content in the unconsolidated, high-porosity surface sediments (0.5 m) is most probably connected with active diffusion and matter exchange between the water-sediment pools.

We investigated changes in the spatial distribution of nitrogen (N) and phosphorus (P) in Lake Peipsi using limnological data from 1970 to 2005. The results show differences in nutrient content between the northern and southern parts of the lake (polarity) and indicate possible causes of eutrophication of this large international lake. The results show a steady gradient in total P (TP) and total N (TN) content along the lake: the northern and deepest part, Lake Peipsi s.s., is significantly less loaded with nutrients than the southern and very shallow part, Lake Pihkva, into which the main inflow, the Velikaya River, discharges. However, the long-term temporal patterns of N and P polarity are different. Statistical analysis, using a parametric functions technique in the framework of general linear analysis provided by the SAS procedures GLM and MIXED, revealed that the polarity of N compounds has been relatively stable over the years and can be related to differences in natural conditions between different parts of the lake. Our study indicates that Lake Peipsi is quite resistant to year-to-year changes in N load, and the in-lake N concentrations are quite stable on a long-term scale. In contrast, the increasing difference in P concentrations between the northern and southern parts of the lake clearly shows that the input of P from the south is increasing. Our results confirm that the anthropogenic input of P is the main reason for the deterioration of the Lake Peipsi ecosystem.

In the 1990s, the nutrient load from the catchment area, carried into the large shallow eutrophic Lake Peipsi (area 3555 km 2 ), diminished in comparison with the 1980s. The aim of the investigation was to analyse statistically biotic response to alterations in nutrient level in the lake following the reduction in external loading. In-lake changes of the relationship between phosphorus and nitrogen compounds and phytoplankton were analysed for 10 years (1992–2001). The content of biogenic elements (total phosphorus, orthophosphate, total nitrogen and ammonia) indicated a decrease and thereafter a stabilization of the parameter values during the observation period. An opposite trend was observed for the nitrite and nitrate ions. The lowest Ntot:Ptot ratio (about 11–13) was registered in 1995–96. However, despite a definite decrease of the nutrient level, the biomass of phytoplankton (particularly cyanobacteria) displayed an increasing trend. Strong and long-lasting (up to October–November) algal blooms were noted in recent years. The structure of the phytoplankton community changed considerably: the share of cyanobacteria (particularly, heterocystous forms) demanding less nutrients increased while the contribution of chlorophytes decreased. The amount of nutrients per biomass unit of different phytoplankton groups decreased. Water level appears to be a significant factor affecting the content of dissolved inorganic nutrients. In particular, NO3N increased and PO4P decreased at higher water level. Large inter-annual water level fluctuations will decrease stability of the ecosystem.

The population of bream in L. Peipsi was studied with respect to age, growth rate, condition factor (according to Fulton) and length-weight relationship in 1994. That autumn the bream population in L. Peipsi consisted of fishes aged from 0+ to 15+. During the first year bream reached an average body length of 7.9 cm (the commercial legal size (30 cm) was usually attained by the end of the 5th–6th year. The condition of bream in this lake was above the average of Estonian lakes. The relatively good growth rate and condition of bream in the lake indicates that the waterbody is appropriate for this fish.

The large but shallow (3,558 km2, up to 15.3 m deep) lake is eutrophic, with Chironomus plumosus and Potamothrix hammoniensis as dominating macroinvertebrates in the profundal. The extensive well-aerated sublittoral with sandy bottom sediments has a mesotrophic appearance and supports a diverse fauna with several oxyphilous species, including a very abundant population of Dreissena polymorpha. The phytophilous fauna is limited to small sheltered areas only. The average abundance of the “small” animals of macrozoobenthos (without big molluscs) was 2,617 ind. m−2, their biomass 12.34 g m−2 (corresponding to 52.2 kJ m−2) in 1964–1994. The same figures for big molluscs (mostly Dreissena) were 304 ind. m−2 and 238 g m−2 in 1964–1994, and even 864 ind. m−2 and 687 g m−2 in 1985–1988, at the time of their special mapping. The sublittoral zone revealed the lowest biomass of “small” animals but the highest biomass of big molluscs. The southern, shallower lake regions, more enriched with nutrients and better protected from wind, revealed a significantly higher biomass of “small” macrozoobenthos in the near-shore zone than the cleaner and open northern part, while no positive effect of enrichment was observed neither in the biomass of profundal zoobenthos nor in that of big molluscs. The production of the “small” macrozoobenthos was calculated as 111 and 53 kJ m−2 during two annual cycles in Lake Peipsi s. s., the most productive period being the autumn overturn. Lake Peipsi-Pihkva has the highest abundance and biomass of macrozoobenthos among the large lakes of North Europe.

Macrozoobenthos of the large (3,558 km2) Lake Peipsi-Pihkva was monitored at 22–24 sampling spots yearly in June 1964–1994 as well as 50 shallow-water profiles in mid-summer 1970, 1980, and 1990. No qualitative changes were observed in the bottom fauna, except for the introduction of a Baikalian gammarid species, Gmelinoides fasciatus. The average total biomass in June (without big molluscs) revealed considerable annual fluctuations, with an insignificant general tendency of increase. The increase was significant in the biomass of several Mollusca (including the highly abundant big clam Dreissena polymorpha), Asellus, Gammaridae, and Hirudinea but not in the most abundant animal groups Chironomidae and Oligochaeta. The low biomass of Ephemeroptera and Hydrachnellae decreased significantly. The mid-summer samples taken from the shallow-water zone in three different years revealed the highest biomass in 1980 and the lowest in 1990 (the latter being probably related to the high water level). A gradual decrease in the biomass of the Ephemeroptera and Hydrachnellae as well as the Oligochaeta, Pisidiidae and Bithynia tentaculata occurred in the shallow-water zone, while the Gammaridae increased on the account of the introduced species. No coincidence was found with the neighbouring Lake Vortsjarv when comparing the annual fluctuations of biomass. A general tendency to a slow increase in total biomass and a decrease in the biomass of the most vulnerable groups Ephemeroptera and Hydrachnellae, probably due to progressing eutrophication, were common for both lakes.