Consistency and flexibility in foraging behaviour play vital roles in organisms’ responses to variable and changing environments. There is a need to understand the causes and consequences of this variation, and to establish how different intrinsic and extrinsic factors alter behaviour at individual, population and species levels. Here I examine individual and population-level variation in the three-dimensional foraging behaviour of a short-ranging benthic-feeding marine predator, the European shag Phalacrocorax aristotelis, focusing on birds breeding in the Farne Islands, UK. Across three years, I found that birds breeding on neighbouring islands were spatially segregated at sea but that this segregation was much stronger in years with higher productivity. I also found that birds displayed individual foraging site fidelity (IFSF), both within and across years, and that females with higher IFSF bred earlier and were in better condition than birds with low IFSF, although this effect was not seen in males. In addition to annual and spatial variation, the characteristics of birds’ foraging trips were also affected by time of day, state of tide and wind speed and direction, with females tending to respond more strongly than males. At a larger spatial scale, the foraging ranges of birds at different colonies around the UK showed a positive relationship with distance to the nearest coastline. These findings highlight the importance of considering variation in foraging behaviour at an appropriate scale and could help improve predictions of individual and population-level responses to future environmental changes.