1. Changes in plankton species diversity and community structure as a result of global warming are of growing concern in ecological studies, as these properties contribute substantially to key ecosystem processes.
2. We analysed the effect of short-term temperature rise and changes in the thermal regime during summer on plankton diversity of the eutrophic and polymictic Müggelsee in Germany, from 26 years of summer records (1982–2007). We tested for changes in community properties, such as species richness, evenness and population size of phyto- and zooplankton, during alternating periods of thermal stratification and mixing, which were between 2 and 8 weeks long. Moreover, we tested for overall long-term temporal trends in annual averages of the community properties during stratified and mixed events.
3. We found that the overall number of stratification events increased significantly across the study period. When the lake was stratified, consistently higher surface water temperatures and lower epilimnetic nutrient concentrations were found. As the length of thermal stratification increased, the phytoplankton shifted towards a higher proportion of buoyant cyanobacteria capable of N-fixation (Aphanizomenon, Anabaena). Diatoms were at a disadvantage because of high temperature, exceeding their upper lethal limit and sedimentation losses. Zooplankton species with high thermal tolerances (i.e. Thermocyclops oithonoides, Thermocyclops crassus) and/or those that grow quickly at high temperatures (i.e. rotifers) became more common.
4. During periods of continuous mixing, the community remained largely unchanged, except for some minor increase in the biomass of diatoms.
5. While a noticeable shift towards N-fixing cyanobacteria was observed with increasing length of stratified events, and rotifers and copepods became the main predators, there were minimal changes in diversity, except for an increase in cyclopoid copepods and a decrease in diatom diversity. As for cyanobacteria, the net short-term effect on their diversity was neutral as a result of species replacements. In the long term, however, the diversity of cyanobacteria and cladocerans declined while that of rotifers increased.
6. Overall, our study presents a cautionary example of how we might fail to foresee the impact of climate-induced changes on ecosystem processes if we restrict our studies to seasonal or yearly temporal scales, thus neglecting the impact of substantial changes operating at smaller temporal scales.