The North Sea is one of the most biologically productive ecosystems in the world and supports important fisheries. Climate-induced changes occurred in the pelagic ecosystems of the North Sea during the 1980s. These changes, which have been observed from phytoplankton to fish and among permanent (holoplankton) and temporary (meroplankton) plankton species, have resulted in alterations in plankton community composition and seasonality. Until now, the effects of climate-driven changes on biological linkages between pelagic and benthic ecosystems have not been examined. The present study indicates that changes in benthic organisms could have a profound effect on the trophodynamics of the pelagos. We demonstrate this by analyses of a long-term time series of North Sea plankton and sea surface temperature data. We discover that pronounced changes in the North Sea meroplankton, mainly related to an increased abundance and spatial distribution of the larvae of a benthic echinoderm, Echinocardium cordatum, result primarily from a stepwise increase in sea temperature after 1987 that has caused warmer conditions to occur earlier in the year than previously. Key stages of reproduction in E. cordatum, gametogenesis and spawning, appear to be influenced by winter and spring sea temperature and their larval development is affected by the quantity and quality of their phytoplankton food. Our analyses suggest that a new thermal regime in the North Sea in winter and spring may have benefited reproduction and survival in this benthic species. As a result, E. cordatum may be altering the trophodynamics of the summer pelagic ecosystem through competition between its larvae and holozooplankton taxa.