The spatial and temporal extent of summer hypoxia (dissolved oxygen [DO] concentration ≤ 2 mg/L) in Chesapeake Bay and its tributaries has been increasing for decades, consequently affecting fish distribution and abundance by shifting biomass to non-hypoxic habitats. Hypoxia in coastal waters impacts food web dynamics, thereby limiting ecosystem productivity and affecting regional fisheries. Additionally, laboratory studies of Atlantic Croakers Micropogonias undulatus have shown that hypoxia serves as an endocrine disruptor, reducing the production of the yolk precursor vitellogenin as well as affecting other biochemical pathways. Reproductive potential is therefore lower in hypoxia-exposed Atlantic Croakers than in fish that are taken from normoxic conditions. We examined field-caught Atlantic Croakers from three Chesapeake Bay tributaries with different DO levels to evaluate patterns in the lipid content of somatic and gonadal tissues. We found that somatic lipid content was not affected by the presence of hypoxia, whereas ovarian lipid content was significantly affected by the severity of hypoxia. Furthermore, Atlantic Croakers that were exposed indirectly to mild hypoxia (lasting hours to days) exhibited greater ovarian lipid content than fish that were captured from normoxic sites. As expected, severe hypoxia reduced the ability of Atlantic Croakers to accumulate lipids in their ovaries, likely affecting reproductive output. Stock assessment models that ignore the effects of hypoxia may yield overly optimistic production estimates for hypoxia-exposed populations, particularly if environmentally invariant fecundity and growth are assumed.