Mangrove forests are impacted by a large range of anthropogenic activities that challenge their functioning. For example, domestic wastewater (WW) discharges are known to increase vegetation growth but recent studies indicate that they have negative effects on benthic macrofauna, especially on mangrove crabs, these ecosystem engineers playing a key role on the functioning of the mangrove. In experimental areas regularly receiving WW at low tide (Mayotte Island, Indian Ocean), a drastic decrease in burrowing crab density has been reported. In this context, the individual behavioural and physiological responses of the fiddler crab Paraleptuca chlorophthalmus exposed to short-term (6 h) pulse of WW and ammonia-N (as a potential proxy of WW) were investigated. This species is one of the most sensitive to WW within the mangrove crab community. For the behavioural experiment, crabs could choose between the aquatic and aerial environment. Individual metabolic rate (O2 consumption) was monitored after 6 h of exposure in WW or ammonia-N. Aerobic and anaerobic metabolic markers (citrate synthase and lactate dehydrogenase activities, respectively) were also evaluated. Results indicate that crabs exposed to WW are more active and mobile than controls after 3 h. Crabs actively emersed from WW and reduced their activity and mobility after 6 h. A higher metabolic rate in WW occurred immediately (t = 0 h), 3 and 6 h after WW exposure, with also, a burst in aerobic bacterial consumption in WW, but no effect of ammonia-N. No effect of WW or ammonia-N was observed on enzymatic aerobic and anaerobic metabolic markers. Therefore, short-term pulses with domestic polluted wastewater trigger quick behavioural and metabolic responses that could be deleterious if prolonged. These results could contribute to the understanding of the community-scale changes observed in benthic macrofauna after several years of regular domestic pollution pulses.