Hypoxia (low oxygen) often occurs in aquatic ecosystems that receive effluent from municipal wastewater treatment plants (WWTP). The combination of hypoxia and WWTP effluent could impair fish health, because WWTP effluent contains multiple contaminants that could disrupt the physiological pathways fish use to cope with hypoxia, but the interactive effects of these stressors on fish physiology are poorly understood. We have examined this issue by exposing mummichog killifish (Fundulus heteroclitus) to hypoxia (5 and 2 kPa O2) and/or 100% WWTP effluent for 21 days in a full factorial design. We then measured hypoxia tolerance, whole-animal metabolism, gill morphology, haematology, and tissue metabolites. In clean water, killifish responded to chronic hypoxia with improvements in hypoxia tolerance, as reflected by increases in time to loss of equilibrium at 0.5 kPa (tLOE). These improvements occurred in association with increases in the exposed surface of gill lamellae that resulted from a regression of interlamellar cell mass (ILCM). Concurrent exposure to wastewater attenuated the increases in tLOE and gill remodeling in chronic hypoxia, and nearly depleted brain glycogen stores. Therefore, exposure to WWTP effluent can disrupt the physiological mechanisms fish use to cope with chronic hypoxia and impair hypoxia tolerance. Our research suggests that the combination of stressors near WWTPs can have interactive effects on the physiology and health of fish.