The 30 km² net-pen aquaculture in East Lake Taihu was cleared in 2019, ending its 34 years history of net-pen aquaculture breeding. The temporal-spatial differences and influencing factors of water quality at 14 monitoring sites during the period of 30 years' (1990-2021) net-pen aquaculture were analyzed. The results showed that the variations of nutrient concentrations in East Lake Taihu in the past 30 years varied with the changes of aquaculture structures (from fish to crab) and aquaculture scales (from excessive utilization to net-pen aquaculture rectification and demolition). The water quality of breeding crabs in net is better than that of breeding fish, owing to the effective management of aquatic plants and mixed breeding pattern. However, as the increase in the intensity of net-pen aquaculture, the water quality degraded. The reduction of the scales of net-pen aquaculture could help improve water quality. The concentrations of total nitrogen (TN), total phosphorus (TP), the permanganate index (COD_Mn) and chlorophyll-a (Chl.a) increased from 0.53 mg/L, 0.014 mg/L, 3.58 mg/L and 2.90 μg/L in 1990 to 1.87 mg/L, 0.128 mg/L, 5.72 mg/L and 28.09 μg/L in 2021, respectively. TN was the main pollution factor. The concentrations of TN, TP, phosphate and suspended solid (SS) in the former net-pen areas and lake center area maintained and unchanged in the past three decades owing to higher aquatic vegetation coverage. The transparency (SD) in the former net-pen areas maintained at 0.8 m. The concentrations of TN, TP, Chl.a, COD_Mn and SS at the sites of Taipu River Estuary and Dongjiaozui showed an increasing trend, while the SD at these sites decreased significantly. The average concentrations of Chl.a at the sites of Taipu River Estuary and Dongjiaozui were significantly positively correlated with the water discharges of the Taipu River. The removal of net-pen, the increase of water discharges and the disappearance of aquatic vegetations increased the hydrodynamic effect. The hydrodynamic effect and the release of nutrients from the sediments in the former net-pen areas resulted in the significant increase of nutrient concentrations in the southern parts of East Lake Taihu. The nutrient concentrations in East Lake Taihu were high in summer and autumn and low in winter and spring since all the net-pen aquaculture was closed down. The implications of this study to other lakes are, in order to ensure the restoration of healthy and natural macrophytic ecosystem patterns, the regulations of aquatic plant resources to be carried out as early as possible so as to strengthen water purification, monitoring of the ecological lake environment, establishing ecological archives, and creating new fishery models.