We evaluate the effects of total ammonia nitrogen-N (TAN) exposure for 72 h on (Na+,K+)- and V(H+)-ATPase activities and on their subunit expressions in gills of the diadromous freshwater shrimp Macrobrachium amazonicum. Specific (Na+,K+)- and V(H+)-ATPase activities increased roughly 1.5- to 2-fold, respectively, after exposure to 2.0 mmol L−1TAN. Quantitative RT-PCR analyses revealed a 2.5-fold increase in V(H+)-ATPase B subunit mRNA expression while (Na+,K+)-ATPase alpha-subunit expression was unchanged. Immunohistochemical analyses of the gill lamellae located the (Na+,K+)-ATPase throughout the intralamellar septal cells, independently of TAN concentration, while the V(H+)-ATPase was located in both the apical pillar cell flanges and pillar cell bodies. Systemic stress parameters like total hemocyte count decreased by 30% after exposure to 2.0 mmol L−1TAN, accompanied by increased activities of the oxidative stress enzymes superoxide dismutase, glutathione reductase and glucose-6-phosphate dehydrogenase in the gills. The stress responses of M. amazonicum to elevated TAN include increases in gill(Na+,K+)- and V(H+)-ATPase activities that are accompanied by changes in oxidative stress enzyme activities, immune system effects and an increase in gill V(H+)-ATPase gene expression. These findings likely underpin physiological effects in a crustacean like M. amazonicum that exploits multiple ecosystems during its life cycle, as well as under culture conditions that may significantly impact shrimp production by the aquaculture industry.