Dissolved organic matter (DOM) is both ubiquitous and diverse in composition in natural waters, but its effects on the branchial physiology of aquatic organisms have received little attention relative to other variables (e.g. pH, hardness, salinity, alkalinity). Here, we investigated the effects of four chemically distinct DOM isolates (three natural, one commercial, ranging from autochthonous to highly allochthonous, all at ∼6 mg C l) on the physiology of gill ionoregulation and nitrogenous waste excretion in zebrafish acclimated to either circumneutral (7.0-8.0) or acidic pH (5.0). Overall, lower pH tended to increase net branchial ammonia excretion, net K + loss and [ 3 H]PEG-4000 clearance rates (indicators of transcellular and paracellular permeability, respectively). However, unidirectional Na + efflux, urea excretion and drinking rates were unaffected. DOM sources tended to stimulate unidirectional Na + influx rate and exerted subtle effects on the concentration-dependent kinetics of Na + uptake, increasing maximum transport capacity. All DOM sources reduced passive Na + efflux rates regardless of pH, but exerted negligible effects on nitrogenous waste excretion, drinking rate, net K + loss or [ 3 H]PEG-4000 clearance, so the mechanism of Na + loss reduction remains unclear. Overall, these actions appear beneficial to ionoregulatory homeostasis in zebrafish, and some may be related to physicochemical properties of the DOM sources. They are very different from those seen in a recent parallel study on Daphnia magna using the same DOM isolates, indicating that DOM actions may be both species and DOM specific.