Larvae of Aedes aegypti, the yellow fever vector, inhabit a variety of aquatic habitats ranging from fresh water to brackish water. This study focuses on the gastric caecum of the larvae, an organ that has not been widely studied. We provide the first measurements of H+, K+, and Na+ fluxes at the distal and proximal gastric caecum, and have shown that they differ in the two regions, consistent with previously reported regionalization of ion transporters. Moreover we have shown that the regionalization of vacuolar H+-ATPase and Na+/K+ -ATPase is altered when larvae are reared in brackish water (30% seawater) relative to fresh water. Measurements of luminal Na+ and K+ concentrations also show a 5-fold increase in Na+/K+ ratio in the caecal lumen in larvae reared in brackish water relative to fresh water, whereas transepithelial potential and luminal pH were unchanged. Calculated electrochemical potentials reveal changes in the active accumulation of Na+ and K+ in the lumen of the gastric caecum of fresh water versus brackish water larvae. Together with the results of previous studies of the larval midgut, our results show that the caecum is functionally distinct from the adjacent anterior midgut, and may play an important role in osmoregulation as well as uptake of nutrients.