Long-term changes in climate are affecting the abundance, distribution and phenology of species across all trophic levels. Short-term climate variability is also having a profound impact on species and trophic interactions. Crucially, species will experience long- and short-term variation simultaneously, and both are predicted to change, yet studies tend to focus on one of these temporal scales. Apex predators are sensitive to long-term climate-driven changes in prey populations and short-term effects of weather on prey availability, both of which could result in changes of diet. We investigated temporal trends and effects of long- and short-term environmental variability on chick diet composition in a North Sea population of European shags Phalacrocorax aristotelis between 1985 and 2014. The proportion of the principle prey, lesser sandeel Ammodytes marinus, declined from 0.99 (1985) to 0.51 (2014), and estimated sandeel size declined from 104.5mm to 92.0mm. Concurrently, diet diversification increased from 1.32 to 10.05 prey types year-1, including Pholidae, Callionymidae and Gadidae. The relative proportion of adult to juvenile sandeel was greater following low Sea Surface Temperatures in the previous year. In contrast, the Pholidae proportion and Prey Richness were higher following high Sea Surface Temperatures in the previous year. Within a season, the proportion of sandeel in the diet was lower on days with higher wind speeds. Crucially, our results showed that diet diversification was linked to trends in temperature. Thus, predicted changes in climate means and variability may have important implications on diet composition in the future, with potential consequences for population dynamics.