Patterns of larval supply and larval condition at metamorphosis play key roles in the structure and dynamics of marine populations. Hence, biological and environmental conditions driving the dispersion of larval individuals, shape early life phenotypes, and influence their survival and post-settlement success. We performed a study over two consecutive years at Ria de Aveiro (Portugal), a coastal lagoon influenced by upwelling regimens in the North-eastern Atlantic. This study assessed the effect of contrasting oceanographic conditions on larval supply and larval traits at metamorphosis of the green crab Carcinus maenas. Crab megalopae were daily sampled and monitored in the laboratory until metamorphosis. Environmental conditions experienced by larvae in the field were estimated considering their expected planktonic larval duration, which was calculated for each individual using the size at metamorphosis and the average water temperature during larval development. Presence/absence, megalopa supply, and larval size were posteriorly modelled using generalized linear mixed models. The analysis of the two consecutive years showed haphazard patterns, revealing that both larval supply and phenotypic traits changed during and between supply seasons. The lunar cycle and environmental conditions were identified as drivers of the presence and supply of megalopae. Settlement events with weak upwelling index were influenced by sea temperature, while intense and constant upwelling events conditioned megalopa supply and performance at metamorphosis. In 2013, megalopae invaded the coastal lagoon in a more advanced physiological stage than in 2012 and/or under better nutritional conditions, probably due to stronger and more constant upwelling events during their pelagic larval life. Our results show that oceanographic processes stimulating upwelling and secondary production are sources of phenotypic variation at settlement, influencing both early benthic performance and adult population dynamics of marine organisms with bi-phasic life cycles.