Trawling fisheries cause in their path uncounted impacts, including direct and indirect effects. This study aimed to evaluate the impact of artisanal trawls on the food availability and its possible impact on the diet of two commercial crustacean species, the pink-shrimp Penaeus paulensis and the blue crab Callinectes sapidus. Two mesocosms were constructed (control and simulated fishing), where sediment samples were collected to analyze the zoobenthos, sediment grain sizes and the percentage of organic matter. Sediment samples were separated into two strata (0–5 and 5–10 cm depth) to evaluate the vertical structure of the fauna, the availability of prey and possible shifts in these patterns after trawling. The Prey-Specific Index of Relative Importance was used in stomach contents analyses. Significant decreases in the percentage of organic matter were observed before and after trawling. Perturbations caused by trawling activities resulted in alterations on the superficial layer, with significant changes in zoobenthos total abundance induced by resuspension and settlement of organisms in other places. Changes in the abundance and richness of zoobenthic organisms caused by trawling were reflected in the diet of pink shrimp and blue crab. A decrease in the main ingested organisms and an increase in the ingestion of more refractory and less energetic items (mainly plants) occurred. Overall, there was a significant effect of trawling on benthic organisms, in particular cases reflected in the predators stomach content, further confirming the impact of trawling on estuarine trophic webs.