Lake eutrophication is a main water environmental problem. When the extraneous nutrients are effectively controlled, nutrients in water mainly source from endogenous release from the sediment. In situ passivation is an important pollution control technique for endogenous pollution in lakes or reservoirs. This study focused on Qianling Lake, a cascade-channel lake in Southwest China polluted by phosphorus (P), which was selected for an in situ passivation project using a novel Al-based passivator on the polluted water area. Accordingly, the release of endogenous nutrients from the sediment can be controlled to remediate the polluted water, and the remediation effect and ecological risk of the passivation were evaluated. The results showed that after 12 months of passivation, the release of P from the sediments can be effectively inhibited. Concentrations of total P (TP) and Chl-a within water of the passivation area were reduced by approximately 80% and 70%. Meanwhile, water transparency and the content of dissolved oxygen were remarkably enhanced. The application of the passivator remarkably improved the water quality. P in water and at the sediment-water interface was fixed on the surface of sediment in the form of Al-combined state. This passivator exhibits favorable P-controlling performance in the restoration of lakes and reservoirs polluted by endogenous P. This aluminum-modified clay is an effective passivator for remediation of internal P pollution in potentially similar lakes and reservoirs.