Coastal upwelling ecosystems support some of the most productive fisheries of the planet together with a large shellfish aquaculture sector that depends on oceanographic processes to deliver planktonic larvae to replenish and feed the farmed stock. Coastal shellfish aquaculture operations in Chile and Perú have experienced large interannual fluctuations in larval supply over the past decade, yet the drivers of such variability remain unidentified. We focused on the effects of environmental variability on larval supply of the farmed Peruvian bay scallop Argopecten purpuratus in a bay in northern Chile (Tongoy Bay, 30∘ S) that accounts for over 90% of countrywide landings. We examined the hypothesis that the environmental processes governing larval supply were shared with wild benthic invertebrates with planktonic larval development and compared time series of larval abundance for the scallop with larval supply rates to benthic populations of two well-studied wild intertidal species: the Chthamalid barnacle Jehlius cirratus and the purple mussel Perumytilus purpuratus. To this end, we examined the cross-correlation of larval supply to environmental variability using MODIS satellite fields of sea surface temperature (SST) chlorophyll-a concentration (chl-a) and fluorescence line height (nFLH), together with three climate indices relevant for the south east Pacific sector: the Southern Oscillation index (SOI), the Pacific Decadal Oscillation (PDO) and the Antarctic Oscillation Index (AAO). Our results showed that over the five-year study period (2009–2013), patterns of larval supply to the scallop population were related to interannual variability in the environmental processes as captured by their Empirical Orthogonal Functions (EOFs), likely to adult condition before spawning. Surprisingly, larval supply for none of the wild species showed a clear association to the EOFs. In contrast, scallops and wild species showed significant association to lower frequency climate variability as captured by the SOI and the PDO, but not the AAO. Results suggest that larval supply patterns to Tongoy Bay may be modulated by regional patterns of climatic variability, particularly of tropical origin. Thus, changes in coastal oceanography associated with ongoing changes in global climate could have strong and lasting effects on the supply of seedstock for wild and cultivated species across this eastern boundary coastal system and argue for the establishment of long-term ocean observing and early warning systems along the region.