Mangrove crabs are ecosystem engineers through their bioturbation activity. On Mayotte Island, the abundance of Neosarmatium africanum decreased in wastewater-impacted areas. Previous analyses showed that global crab metabolism is impacted by wastewater, with a burst in O-2 consumption that may be caused by osmo-respiratory trade-offs since gill functioning was impacted. As the hepatopancreas is a key metabolic organ, the purpose of this study was to investigate the physiological effects of wastewater and ammonia-N 5-h exposure on crabs to better understand the potential trade-offs underlying the global metabolic state. Catalase, superoxide dismutase, glutathione S-transferase, total digestive protease, and serine protease (trypsin and chymotrypsin) activities were assessed. Histological analyses were performed to determine structural modifications. No effect of short-term wastewater and ammonia-N exposure was found in antioxidant defenses or digestive enzyme activity. However, histological changes of B-cells indicate an increase in intracellular digestive activity through higher vacuolization processes and tubule dilation in wastewater-exposed crabs.