Human activities present aquatic species with numerous of environmental challenges, including excessive nutrient pollution (nitrate) and altered pH regimes (freshwater acidification). In isolation, elevated nitrate and acidic pH can lower the blood oxygen-carrying capacity of aquatic species and cause corresponding declines in key functional performance traits such as growth and locomotor capacity. These factors may pose considerable physiological challenges to organisms but little is known about their combined effects. To characterise the energetic and physiological consequences of simultaneous exposure to nitrate and low pH, we exposed spangled perch (Leiopotherapon unicolor) to a combination of nitrate (0, 50 or 100 mg L−1) and pH (pH 7.0 or 4.0) treatments in a factorial experimental design. Blood oxygen-carrying capacity (haemoglobin concentration, methaemoglobin concentrations and oxygen equilibrium curves), aerobic scope and functional performance traits (growth, swimming performance and post-exercise recovery) were assessed after 28 days of exposure. The oxygen-carrying capacity of fish exposed to elevated nitrate (50 and 100 mg L−1) was compromised due to reductions in haematocrit, functional haemoglobin levels and a 3-fold increase in methaemoglobin concentrations. Oxygen uptake was also impeded due to a right shift in oxygen–haemoglobin binding curves of fish exposed to nitrate and pH 4.0 simultaneously. A reduced blood oxygen-carrying capacity translated to a lowered aerobic scope, and the functional performance of fish (growth and swimming performance and increased post-exercise recovery times) was compromised by the combined effects of nitrate and low pH. These results highlight the impacts on aquatic organisms living in environments threatened by excessive nitrate and acidic pH conditions.