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.