Climate change is predicted to have widespread impacts on freshwater lake and reservoir nutrient budgets by altering both hypolimnetic hypoxia and runoff, which will in turn alter the magnitude of internal and external nutrient loads. To examine the effects of these potential climate scenarios on nitrogen (N) and phosphorus (P) budgets, we conducted a whole-catchment manipulation of hypolimnetic oxygen conditions and external loads to Falling Creek Reservoir (FCR), an old, eutrophic reservoir in a reforested catchment with a history of agricultural land use. Throughout 2 years of monitoring, internal N and P loading during hypoxic conditions dominated the hypolimnetic mass of nutrients in FCR, regardless of changes in external loading. FCR commonly functioned as a net sink of N and P, except during hypoxic conditions, when the reservoir was a net source of ammonium ( NH+4 ) to downstream. We observed extremely high nitrate–nitrite ( NO−3−NO−2 ), soluble reactive P (SRP), total nitrogen (TN), and total phosphorus (TP) retention rates, indicating that the reservoir served as a sink for greater than 70% of NO−3−NO−2 inputs and greater than 30% of SRP, TN, and TP inputs, on average. Our study is notable in the length of time since reforestation (>80 years) that a reservoir is still exhibiting high N and P internal loading during hypoxia, potentially as a result of the considerable store of accumulated nutrients in its sediment from historical agricultural runoff. Our whole-catchment manipulations highlight the importance of understanding how multiple aspects of global change, waterbody and catchment characteristics, and land use history will interact to alter nutrient budgets in the future.