<p>In the Amazon basin, the white- and blackwater rivers have marked variability in their natural physicochemical characteristics, which impose differential physiological constraints that shape aquatic biodiversity. <i>Thriportheus albus</i> is a Characiform fish widely distributed throughout the different types of water in Amazon basin, with two distinct and isolated populations, a whitewater and a blackwater/clearwater population. In this study we compare blood biochemical, hematological parameters and the activity of the main ionoregulatory enzymes in gills and kidneys of <i>T. albus</i> populations from the blackwaters of Rio Negro and in the whitewater’s of Rio Solimões. <i>T. albus</i> from the blackwaters showed a higher hemoglobin concentration, hematocrit and levels of Na and Ca in blood compared to fish from the whitewater. Remarkably, the activity of both Na⁺/K⁺-ATPase and NEM sensitive-ATPase were significantly higher in the gills and kidneys of <i>T. albus</i> from blackwater. A Principal Component Analysis (PCA) revealed that up regulation of both transporters were closed related to increased blood parameters in <i>T. albus</i> from blackwater, suggesting that physiological adjustments in mechanisms for ionic uptake in gills and reabsorption in kidney aid fish to avoid internal disturbances in blood ionic levels, and optimize oxygen transport, to cope with the extremely low ionic content and high acidity found in Rio Negro. Altogether, these findings indicate that physiological adjustments in hematological parameters, and in the control of the gills and kidneys functions exert a central role in the adaptation of <i>T. albus</i> to the acidic ion-poor conditions of Amazonian blackwaters.</p>