The effect of dissolved organic carbon (DOC) against the burden of low pH was assessed in silver catfish Rhamdia quelen through the gills. A commercial humic acid (HA) was used as the source of DOC at 0 (control), 10, 25, and 50 mg/l. For each HA concentration, two pH levels were tested: 6.5 (control) and 5.5. After 40 days of exposure, the gills were removed and morphological variables were analyzed through light and scanning electronic microscopy. The low water pH caused a reduction in the length of filaments, number of lamellae, and gill respiratory surface area (GRSA) and an increase in chloride cells (CCs) number in the filament epithelium. When HA was added to the test water, GRSA increased and CCs proliferated in lamellae, suggesting ionic and respiratory disturbances. Scanning electronic microscopy revealed that CC morphometric variables, that is, apical area, fractional area, and density, were undisturbed by the pH reduction, but increased in the presence of HA. This study indicates that the commercial HA did not protect silver catfish against low pH stress. Instead, it caused changes that may affect vital processes such as ion regulation and ventilation and, consequently, reduce growth.