Aedes aegypti commonly inhabit ammonia-rich sewage effluents in tropical regions of the world where the adults are responsible for the spread of disease. Studies have shown the importance of the anal papillae of A. aegypti in ion uptake and ammonia excretion. The anal papillae express ammonia transporters and Rhesus (Rh) proteins which are involved in ammonia excretion and studies have primarily focused on understanding these mechanisms in freshwater. In this study, effects of rearing larvae in salt (5 mmol l −1 NaCl) or ammonia (5 mmol l −1 NH 4 Cl) on physiological endpoints of ammonia and ion regulation were assessed. In anal papillae of NaCl-reared larvae, Rh protein expression increased, NHE3 transcript abundance decreased and NH 4 + excretion increased, and this coincided with decreased hemolymph [NH 4 + ] and pH. We propose that under these conditions, larvae excrete more NH 4 + through Rh proteins as a means of eliminating acid from the hemolymph. In anal papillae of NH 4 Clreared larvae, expression of an apical ammonia transporter and the Rh proteins decreased, the activities of NKA and VA decreased and increased, respectively, and this coincided with hemolymph acidification. The results present evidence for a role of Rh proteins in acid-base balance in response to elevated levels of salt, whereby ammonia is excreted as an acid equivalent.