How to improve habitat quality for wildlife is of particular importance in areas dedicated to food production, due to increasing pressures of global demands associated to human population growth. Semi-intensive aquaculture ponds can provide a potentially important foraging habitat for migratory shorebirds throughout the non-breeding season. Therefore, understanding the availability of benthic invertebrates in aquaculture ponds will help to identify proper management decisions for shorebird conservation. We used an exclosure experiment during the first three days after shrimp harvesting at semi-intensive aquaculture ponds in north-west Mexico to assess shorebird predation on benthic invertebrates. We found that shorebird predation did not deplete total benthic invertebrate density (particularly polychaete worms), but significantly affected the prey size distributions and biomass in the ponds during a short-time window of just three days. Shorebirds removed 0.6 g ash-free dry weight m−2, equivalent to 43% of the initial biomass and showed high selectivity for polychaetes larger than >40 mm as prey, potentially explaining the absence of large polychaetes at the end of the experiment. This depletion was the likely cause of the daily decrease observed in overall density of foraging shorebirds at recently harvested ponds. These results can serve to identify management actions that allow an extended use of semi-intensive aquaculture ponds as foraging sites for migratory shorebirds during the non-breeding season, with potential applications to develop standards for a friendlier aquaculture management.