Anthropogenic sources increase freshwater salinity and produce differences in constituent ions compared with natural waters. Moreover, ions differ in physiological roles and concentrations in intracellular and extracellular fluids. Four freshwater taxa groups are compared, to investigate similarities and differences in ion transport processes and what ion transport mechanisms suggest about the toxicity of these or other ions in freshwater. Although differences exist, many ion transporters are functionally similar and may belong to evolutionarily conserved protein families. For example, the Na+/H+-exchanger in teleost fish differs from the H+/2Na+ (or Ca2+)-exchanger in crustaceans. In osmoregulation, Na+ and Cl− predominate. Stenohaline freshwater animals hyperregulate until they are no longer able to maintain hypertonic extracellular Na+ and Cl− concentrations with increasing salinity and become isotonic. Toxic effects of K+ are related to ionoregulation and volume regulation. The ionic balance between intracellular and extracellular fluids is maintained by Na+/K+-adenosine triphosphatase (ATPase), but details are lacking on apical K+ transporters. Elevated H+ affects the maintenance of internal Na+ by Na+/H+ exchange; elevated HCO3− inhibits Cl− uptake. The uptake of Mg2+ occurs by the gills or intestine, but details are lacking on Mg2+ transporters. In unionid gills, SO42− is actively transported, but most epithelia are generally impermeant to SO42−. Transporters of Ca2+ maintain homeostasis of dissolved Ca2+. More integration of physiology with toxicology is needed to fully understand freshwater ion effects.