Blackwater systems, characterized by low pH, low ion concentrations, and a high concentration of dissolved organic carbon (DOC) are found globally. The most notable are the blackwaters of the Amazon River, one of the most biodiverse ecosystems worldwide. The harsh water chemistry is toxic to most freshwater fish, while endemic species including the dwarf cichlid, thrive due to the protective effects provided by DOC. Natural DOCs were collected in the Amazon basin: a DOC-rich, low pH, ion-poor “blackwater” from the Rio Negro and a water lower in DOC but higher in pH and ion concentration from the Rio Solimoes. Due to the complexity and heterogeneity of DOCs, three model compounds; tannic acid, bovine serum albumin and sodium dodecyl sulfate, with known chemical properties were chosen based on the criteria that they structurally resemble or functionally behave like certain chemical moieties of humic acid, a major component of natural DOCs. Dwarf cichlids were exposed to control water, or one of the five DOCs at pH 7 or pH 4 and net Na+ and Cl- fluxes, ammonia-N and urea-N excretion rates and gill paracellular permeability were measured. Our results demonstrate that the effects of the natural DOCs are related to their chemical structure and water pH. This contributes to understanding the properties of DOC that are interacting with the gill and how this interaction influences ion and water transport in acidic waters (NSERC, ADAPTA, CNPQ).