During the study period 1997–2007, the duration of the ice cover of Lake Peipsi, the largest freshwater lake in Estonia, was variable. The ice-break took place in mid-April instead of generally in May. Compared with data from 1960s onwards, a trend of shortening of the duration of ice-cover period is evident. In under-ice phytoplankton, diatoms, cryptophytes and flagellated chlorophytes predominated from March to June. In zooplankton, while thermophobic rotifers dominated in densities, copepods were dominant in biomass. The monthly sum of positive water temperatures correlated with the zooplankton in the following month and duration of the ice cover correlated with the biomass of all different zooplankton groups in May and June. The sum of water temperatures in April, May and June was positively correlated with the biomass of cladocerans and copepods, and negatively with the biomass of winter rotifers. Mild winters affected nitrogen and silica concentration positively and phosphorus concentration negatively.