Onshore pond-based aquaculture occupies a large proportion of coastal fisheries and is vulnerable to marine flooding. One common adaptation strategy is constructing sluices along inlets to prevent flooding. The efficacies of sluices typically depend on gate operation, associated risks, and flooding processes. However, few studies were focused on inundation characteristics and mitigation measures for valuable aquaculture farms. To assess the effectiveness of sluices in flood mitigation, we simulated storm surge inundation processes in a coastal aquaculture farm in the Pearl River Delta, where storm surges frequently occurred. The newly constructed sluice can substantially reduce the extent and severity of flood inundation. The antecedent water levels in fish ponds significantly affected the inundation processes, and a water level of −0.5 ∼ 0 m below mean sea level was a recommended value for reducing inundation risk. Our modeling results regarding the effect of the sluice and antecedent water levels on mitigating flood inundation will provide a reference for flood control of onshore aquaculture farms.