In the last 40 years, the shallow steppe lake, Neusiedler See, was ice covered between 0 and 97 days. The North Atlantic Oscillation (NAO) as well as the Mediterranean Oscillation affected the lake and its conditions during winter. Both climate indices correlated negatively with the duration of ice cover and the timing of ice-out. Average winter phytoplankton biomass increased from less than 0.2 (0.05–0.84) mg FM l⁻¹ in the late 1960s/beginning of 1970s to 3.1 (1.72–5.61) mg FM l⁻¹ in the years 2001–2004. The increase in annual winter biomass of phytoplankton was associated with a significant shift in the composition of the algal assemblage. In the winter 1997/1998, diatoms contributed between 40 and 80% to the phytoplankton biomass while in 2006/2007 cyanoprokaryotes contributed 46%. Mean chlorophyll-a concentrations during winter were significantly correlated with those of total phosphorus (P_tot). Together with cold-water species (rotifer Rhinoglena fertöensis), perennial, eurythermal ones (copepod Arctodiaptomus spinosus) contributed to the zooplankton community. High zooplankton numbers were encountered when rotifers, particularly when densities of Rhinoglena fertöensis were high (r ² = 0.928). Zooplankton abundance and biomass varied from year to year but correlated positively with Chl-a (biomass − r ² = 0.69; numbers − r ² = 0.536). Winter zooplankton populations were primarily influenced by winter conditions, but in early winter also by survival of autumn populations, i.e., the more adults of Arctodiaptomus spinosus survived into winter, the higher was the zooplankton biomass in early winter. Phyto- and zooplankton dynamics in shallow lakes of the temperate region seem to critically depend on the biomass in autumn and on winter conditions, specifically on ice conditions and thus are related to climate signals such as the NAO.