Abstract Across diverse systems, nutrient loading from anthropogenic sources into aquatic systems has increased over the past century. Such nutrient inputs may enhance system productivity and thereby increase resource availability but may also lead to undesirable conditions such as hypoxic zones. We examined the habitat quality trade‐offs associated with increases in phosphorus in a model system (Lake Erie, North America) with a history of anthropogenic nutrient loading. Using a water quality model and a bioenergetics growth rate potential model with fine vertical and temporal resolution, we assessed how the quality of habitat for multiple species of adult and juvenile fish changed across a range of phosphorus loading scenarios and across 19 different meteorological years. Increases in phosphorus loading increased invertebrate prey biomass, but also increased the duration and extent of the mid‐summer hypoxic zone. In general, phosphorus loading caused overall habitat quality to decline and only increased peak habitat quality (i.e., spatio‐temporal locations where temperature and prey abundance were already above average), but responses were species‐ and life‐stage specific. One challenge in ascertaining the effects of nutrient loading on fish habitat quality is separating the negative effects of hypoxia from the potential positive effects of increased prey densities. Through various model scenarios, we evaluated the individual effects of hypoxia and increased prey availability on fish habitat quality, demonstrating their potentially counter‐balancing effects. That is, the negative effects of low oxygen on fish habitat quality appear more severe if the prospect that increased hypoxia is accompanied by altered prey densities is not accounted for. Despite modelled responses to altered phosphorus loads, habitat quality responded more strongly to variation in annual meteorological conditions. Annual meteorological conditions such as temperature, vertical mixing, and timing of phosphorus loading had a greater effect on habitat quality for all species and life‐stages than changes in annual amount of phosphorus loading. This limited effect of changes in phosphorus loading on habitat quality probably partially reflects our focus on short‐term (1‐year) changes in loading. Thus, nutrient abatement programmes may not lead to obvious, rapid positive habitat quality responses, as short‐term meteorological effects may overwhelm effects related to nutrient reduction and changes in prey densities may partially offset the benefits of decreased hypoxic conditions.