Abstract Dissolved organic matter (DOM), a heterogeneous substance found in all natural waters, has many documented abiotic roles, but recently, several possible direct influences of DOM on organism physiology have been reported. However, most studies have been carried out with a limited number of natural DOM isolates or were restricted to the use of commercial or artificial humic substances. We therefore employed three previously characterized, chemically-distinct natural DOMs, as well as a commercially available humic acid (Aldrich, AHA), at circumneutral (7–8) and acidic pH (~5), to examine DOM effects on whole-body Na+ concentration, unidirectional influx and efflux rates of Na+, and ammonia and urea excretion rates in Daphnia magna. Whole-body Na+ concentration, Na+ influx, and Na+ efflux rates were all unaffected regardless of pH, suggesting no influence of the various natural DOMs on active uptake and passive diffusion of Na+ in this organism. Ammonia and urea excretion rates were both increased by low pH. Ammonia excretion rates were reduced at circumneutral pH by the most highly colored, allochthonous DOM, and at low pH by all three natural DOMs, as well as by the commercial AHA. Urea excretion rates were not influenced by the presence of the various DOMs in circumneutral solutions, but were attenuated by the presence of two allochthonous DOM sources (isolated from Bannister Lake and Luther Marsh) at acidic pH. The observed reductions may be attributed partially to the higher buffering capacities of natural DOM sources, as well as their ability to interact with biological membranes as estimated by a new measure calculated from their acid–base titration characteristics, the Proton Binding Index (PBI).