Sandy beaches are being threatened by a changing climate. However, the effects of this changing environment, including warming, on these ecosystems, have hitherto been tentative and qualitative. Using concurrent long-term (1984−2007) observations on abundance and individual size, together with laboratory examinations of body abnormalities (morphological anomalies and epibionts), we provide evidence that the sandy beach yellow clam Mesodesma mactroides of the Uruguayan coast has responded to climate change. Regional sea surface temperature anomalies (SSTA) showed an increasing trend through time, with positive values after 1997. The position of the warm water front (20°C isotherm), a proxy of tropical waters, showed a long-term poleward shift rate of ca. 9 km yr −1. Clam abundance (total and discriminated by population component) decreased through time and was inversely related to variations in SSTA, with higher abundance during cold periods. Length frequency distributions (LFDs) showed polymodal size structures with fully represented clam population components in cool years. By contrast, LFDs showed fewer size classes and larger clams were virtually absent during warm years. Prevalence of body abnormalities in M. mactroides increased through time and was positively correlated with increasing SSTA, suggesting a link with climate stress. The population dynamics of M. mactroides seems to be driven by climatic forcing, mostly related with warming. Our results demonstrate the implications of climate change in the structure of sandy beach fauna, which could be particularly relevant in ectotherms with cold water affinities. Thus, climate change should be given a high priority in sandy beach conservation planning and management.