Nepenthes pitcher plant species differ in their prey capture strategies, prey capture rates, and pitcher longevity. In this study, it is investigated whether or not interspecific differences in nutrient sequestration strategy are reflected in the physiology and microstructure of the pitchers themselves. Using a non-invasive technique (MIFE), ion fluxes in pitchers of Nepenthes ampullaria Jack, Nepenthes bicalcarata Hook.f., and Nepenthes rafflesiana Jack were measured. Scanning electron microscopy was also used to characterize the distribution of glandular and other structures on the inner pitcher walls. The results demonstrate that nutrient sequestration strategy is indeed mirrored in pitcher physiology and microstructure. Species producing long-lived pitchers with low prey capture rates (N. ampullaria, N. bicalcarata) showed lower rates of NH4+ uptake than N. rafflesiana, a species producing short-lived pitchers with high capture rates. Crucially, species dependent upon aquatic commensals (N. ampullaria, N. bicalcarata) actively manipulated H+ fluxes to maintain less acid pitcher fluid than found in ‘typical’ species; in addition, these species lacked the lunate cells and epicuticular waxes characteristic of ‘typical’ insectivorous congeners. An unexpected finding was that ion fluxes occurred in the wax-covered, non-glandular zones in N. rafflesiana. The only candidates for active transport of aqueous ions in these zones appear to be the epidermal cells lying beneath the lunate cells, as these are the only sites not visibly coated with epicuticular waxes.