Coastal and estuarine habitats function as nurseries for many commercial marine species. In these ecosystems, the hypothesis that food supply limits juvenile fish density and survival has been widely debated. Direct approaches that test this hypothesis in temperate soft-bottom nurseries are data-intensive as they rely on beam trawl to collect juvenile fish and grab or core to collect their prey within the macrobenthic community. Thus, application has often been limited to a few sampling stations and temporal snapshots. However, scientific beam trawl surveys, conducted periodically in nurseries, sample, besides juvenile fish, benthic invertebrates including potential prey species. Using data collected solely from beam trawl surveys, we tested whether food supply limits juvenile fish densities in several French nurseries. First, we validated that data of benthic invertebrates from bottom trawl surveys could be used to estimate an index of benthic prey production, by comparing data collected by grabs and trawls at the same sampling locations. Using this index on an extended trawl dataset, we estimated inter-annual variability of benthic prey production among several nurseries along the coast of the Bay of Biscay. Estimates of benthic prey production index were similar among nurseries, although, these nurseries displayed different local hydrological patterns (currents and residence time). The index was finally used to investigate whether benthic prey production limits young-of-the-year fish density using quantile regressions. We found a significant and positive relationship between the benthic prey production index and young-of-the-year fish densities, including flatfish and round fish species. Hence, our study supports the hypothesis that trophic limitation occurs for juvenile fish in coastal and estuarine nurseries during their first year of life, although other factors likely limit them locally.