Calanus species are perhaps the most investigated planktonic copepods due to their pivotal role supporting pelagic food webs in temperate and cold shelf ecosystems. In the Adriatic Sea, C. helgolandicus is a prominent species of the seasonal bulk of copepods biomass. We here examined temporal changes of C. helgolandicus over the period 1985-2010 in the marine protected area of Mljet Island, south Adriatic Sea. Our results showed close connection between regional and local hydrographic variability, which cascaded down shifting the local environment towards warmer conditions after 1997. C. helgolandicus displayed marked year-to-year variations from the middle 1980s until the late 1990s, followed by a sustained abundance increase in the 2000s, which was concurrent with warmer environmental conditions. The temperature increased further altered the phenology of the species, where the timing of seasonal peak shifted forward ca. two months under higher temperatures. Partitioning effects of forcing factors highlighted a leading role of temperature favoring C. helgolandicus, while negatively affecting chaetognaths abundance, the main copepod predator in the system. These results illustrate a climate-driven top-down control released, which combined with favorable environmental conditions, lead the abundance observed abundance increase of C. helgolandicus in the first decade of 2000s. Sheltered from anthropogenic disturbances, marine protected areas appear as natural laboratories to assess plankton food web responses to changing climate.