The contamination of estuaries by metals can impose additional stresses on estuarine species, which may exhibit a limited capability to adjust their regulatory processes and maintain physiological homeostasis. The mudflat fiddler crab Uca rapax is a typical estuarine crab, abundant in both pristine and contaminated areas along the Atlantic coast of Brazil. This study evaluates osmotic and ionic regulatory ability and gill Na+/K+-ATPase activity in different salinities (<0.5, 25 and 60 ‰ S) and oxygen consumption rates at different temperatures (15, 25 and 35 °C) in U. rapax collected from localities along the coast of São Paulo State showing different histories of metal contamination (most contaminated Ilha Diana, Santos > Rio Itapanhaú, Bertioga > Picinguaba, Ubatuba [pristine reference site]). Our findings show that the contamination of Uca rapax by metals in situ leads to bioaccumulation and induces biochemical and physiological changes compared to crabs from the pristine locality. Uca rapax from the contaminated sites exhibit stronger hyper- and hypo-osmotic regulatory abilities and show greater gill Na+/K+-ATPase activities than crabs from the pristine site, revealing that the underlying biochemical machinery can maintain systemic physiological processes functioning well. However, oxygen consumption, particularly at elevated temperatures, decreases in crabs showing high bioaccumulation titers but increases in crabs with low/moderate bioaccumulation levels. These data show that Uca rapax chronically contaminated in situ exhibits compensatory biochemical and physiological adjustments, and reveal the importance of studies on organisms exposed to metals in situ, particularly estuarine invertebrates subject to frequent changes in natural environmental parameters like salinity and temperature.