In species with complex life cycles, laboratory studies have shown that variations in the traits of settling larvae can affect post-settlement survival and influence recruitment and benthic-pelagic coupling. However, we still know little about the magnitude and spatial scale of natural trait variation. We studied spatial variation in body size and nutritional reserves (carbon, nitrogen and lipids) of settled cyprids of the barnacle Semibalanus balanoides along the coast of West Scotland. We quantified variation among regions (north vs. south: range ~700 km), locations (~50 km), shores (~10 km) and within shores (~10 m). We also evaluated trait responses to gradients in chlorophyll and shore openness and compared swimming vs. settled cyprids in order to infer the likely influence of costs of substratum search on trait variation. Variability between regions was large, with higher trait values (e.g. carbon cyprid-1: 35 to 50% higher) in the north. Most traits correlated negatively with pelagic chlorophyll a (a proxy for larval/juvenile food availability); this counter-gradient pattern suggests an adaptive role of increased reserves, buffering benthic juveniles from low food availability during the critical early post-settlement period. Body size and nitrogen content correlated positively with shore openness; lower than expected carbon content suggest increased costs of substratum search on open shorelines. Higher nitrogen content but lower percent carbon was found in settled vs. swimming larvae, suggesting costs of substratum search at the time of settlement. Overall, we uncovered the spatial scales at which trait variation, shaped by pelagic processes, can affect post-metamorphic survival, recruitment and benthic-pelagic coupling.