We discovered, using transfer functions, that climatic changes in the Atlantic control the abundance of Temora longicornis, a dominant pelagic copepod of the Baltic Sea. The seawater salinity was increasing and copepod numbers were high from 1960s up to 1970s. Then the freshwater runoff started to increase, which resulted in decreasing salinities and abundance of the copepod. At the end of 1990s, runoffs remained at a high level, and the decrease of surface salinities and Temora leveled off. Due to time lags between variables studied, we also make predictions of changes expectable in early 2000s. The total freshwater runoff to the Baltic Sea followed the North Atlantic Oscillation with an immediate lag. Salinity followed the runoff non-linearly with a lag of 4–9 months. Temora longicornis followed the salinity with a lag of 1–3 months. Predicted abundance of T. longicornis will remain low implicating poor feeding conditions for planktivores. Our study points out the importance of physical factors in control of pelagic environments compared to ecological interactions, such as top-down and bottom-up.