The Manila clam Ruditapes philippinarum is one of the most commercially valuable bivalve species worldwide and its range is expanding, facilitated by aquaculture and fishing activities. In existing and new systems, the species may become commercially and ecologically important, supporting both local fishing activities and populations of shorebird predators of conservation importance. This study assessed potential fishing effects and population dynamics of R. philippinarum in Poole Harbour, a marine protected area on the south coast of the UK, where the species is important for oystercatcher Haematopus ostralegus as well as local fishers. Sampling was undertaken across three sites of different fishing intensities before and after the 2015 fishing season, which extends into the key overwintering period for shorebird populations. Significant differences in density, size and condition index are evident between sites, with the heavily dredged site supporting clams of poorer condition. Across the dredge season, clam densities in the heavily fished area were significantly reduced, with a harvesting efficiency of legally harvestable clams of up to 95% in this area. Despite occurring at significantly higher densities and growing faster under heavy fishing pressure, lower biomass and condition index of R. philippinarum in this area, coupled with the dramatic reduction in densities across the fishing season, may be of concern to managers who must consider the wider ecological interactions of harvesting with the interest of nature conservation and site integrity.