At land-sea interface, mangroves are likely to be exposed to pesticides due to agricultural run-offs. In Mayotte Island (Comoros archipelago, Mozambique Channel), dimethoate (DMT) is found in high concentrations in tomatoes, but no data confirm its presence in mangroves. We aimed at screening the presence of DMT in three mangroves of Mayotte at different levels (highest point above crops, village, upstream mangrove, downstream mangrove) and assessing the impact of DMT coupled with reduced salinity on mangrove crab physiology. To do so, we performed 24-h exposures at sublethal concentrations (10 and 100 µg L−1) corresponding to 100 × and 1000 × the environmental standard (no data exist on environmental concentrations), in seawater (SW) and diluted SW (dSW). We exposed male fiddler crab Tubuca urvillei, one of the most common fiddler crabs living in mangrove areas regularly flooded and exposed to agricultural run-offs. Different physiological endpoints were considered: behaviour, acetylcholinesterase (AChE) activity, muscle energy metabolism, DNA oxidative damage and osmoregulatory capacity using hemolymph samples, posterior gills and claw muscle. We confirmed the presence of DMT in one mangrove and the effect of pesticide exposure at the different endpoints. Changes in behavioural and physiological parameters highlighted in this study could warn us of recent pesticide use upstream and help us understand past or future community-level changes in mangrove ecosystems affected by pesticide inputs.