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Water level changes (7-year moving averages) in Lake Võrtsjärv (Estonia) during 1885–2000 were correlated with winter patterns in the North Atlantic Oscillation (NAO) index. In this shallow lake (270 km2, mean depth 2.8 m), where the annual water level amplitude is 1.4 m and the absolute range is 3.2 m, hydrology is the main driving force for the ecosystem. Control of phytoplankton growth was mediated by ice conditions in spring, and by water level in summer and autumn. Winter air temperature similarly influenced the biomass of cyanobacteria and diatoms in spring; while the effect of the ice-cover duration was more pronounced on cyanobacteria. Mean depth of the lake did not affect the phytoplankton biomass in spring, but clearly controlled it in summer and autumn. The direct impact of winter conditions on biological processes was restricted to a short post-winter period, but extended indirectly as the water level for the entire growing season depended strongly on the height of the spring flood peak.

From 1961–2004, surface water temperature in large and shallow Lakes Peipsi and Võrtsjärv in Estonia increased significantly in April and August; respectively 0.37–0.75 and 0.32–0.42 degrees per decade reflecting the changes in air temperature. The average annual amount of precipitation in the catchment increased significantly. Reflecting practices in agriculture and wastewater treatment, nutrient loadings to the lakes increased rapidly in the 1980s and decreased again in the early 1990s. As total nitrogen (TN) loading decreased faster than total phosphorus (TP) loading, the TN/TP ratio in the loadings decreased. Both the increased temperature and low TN/TP ratio favoured the development of cyanobacteria blooms in Lake Peipsi. In Võrtsjärv, where the TN/TP mass ratio is about two times higher than in Peipsi, blooms did not occur. Recently, the TN/TP ratio has shown a tendency of increase in both lakes suggesting a certain reduction of blooms to be expected also in Lake Peipsi. Nutrient dynamics in the lakes followed the changes in loadings, showing the ability of shallow lake ecosystems to react sensitively to changes in catchment management as well as in climate.