The combined effects of warming and overwintering copepod densities on the spring succession of Baltic Sea plankton were investigated using indoor mesocosms. Three zooplankton (1.5, 4 and 10 copepods L-1) and two temperature levels called ∆0°C and ∆6°C (0°C and 6°C above the present day temperature scenario for Kiel Bight) were chosen. Both, the timing and the duration of the protozooplankton (PZP) bloom were significantly affected by temperature, but not by copepod density. In contrast, the bloom intensity of PZP was highly affected by the factors temperature and copepod density and its interaction. This suggests that at elevated temperature conditions PZP grows faster but, at the same time, are subject to higher top-down control by copepods. At low temperatures and low copepod densities, PZP in turn fully escaped from copepod predation. Further changes in the overwintering copepod densities resulted in a strong ciliate suppression of which small-sized ciliates (<30 µm) were especially vulnerable to copepod predation while other PZP size classes remained unaffected. In conclusion, the results presented point at a pivotal regulating role of overwintering copepods under future warming condition. Further, warming was shown to cause a distinct match between phytoplankton and PZP thus strengthening trophic pathways through PZP. Our findings are discussed in the context of the ‘trophic link-sink’ debate by considering potential alterations in the flux of matter and energy up the food web.