Large deep lakes in plateau regions provide crucial ecosystem services but are susceptible to eutrophication due to their long water residence time. To date, the water quality of deep lakes has not received as much attention as that of shallow lakes owing to logistical challenges. This study investigated the seasonal variation and vertical distribution of phosphorus and related environmental variables in a large deep lake in the Yunnan Plateau, China (Fuxian Lake). Generally, the concentrations of total phosphorus (TP, R2 = 0.862), total dissolved phosphorus (TDP, R2 = 0.922), and dissolved inorganic phosphorus (DIP, R2 = 0.889) exhibited a linear increase with the greater water depth, whereas the pH and dissolved oxygen (DO) showed decreasing trends. The TP, TDP, and DIP values were 0.012, 0.006, and 0.004 mg/L, respectively, in surface waters (0.5 m depth), and increased to 0.074, 0.065, and 0.062 mg/L, respectively, at 140.0 m depth. The averaged over ordering method demonstrated that DO and air temperature accounted for a higher proportion of the explained variance of TP, TDP, and DIP in the shallow water layer (0.5–20.0 m). In contrast, DO and pH accounted for a higher proportion of the explained variance of TP, TDP, and DIP in deeper water layers (40.0–150.0 m). As a warm monomictic lake, the higher observed phosphorus concentrations in deeper water and sediment potentially pose a risk of future eutrophication in the Fuxian Lake. Our findings demonstrate that more efficient technical and management measures should be taken to reduce the external phosphorus load to Fuxian Lake, so that the load to and from the sediment will decrease eventually.