Hulun Lake, the largest inland steppe lake in China, is encountering severe water quality degradation. Estuaries play important roles in material and energetic exchange between rivers and lakes. The water quality at the estuaries of Hulun Lake directly reflects the impact of both human activities and natural factors on the lake’s overall water quality, especially during rainfall events. From July 28, 2021, to August 4, 2021, water samples from 62 sites were collected in the three estuaries of Hulun Lake before and after a moderate rainfall event. 13 water parameters, including dissolved oxygen (DO), Turbidity (Tur), Total Nitrogen (TN), Total Phosphorus (TP), Total Organic Nitrogen (TON), and Total Organic Phosphorus (TOP) were measured. The spatio-temporal distribution of water quality in the estuaries was assessed based on water quality index (WQI). Besides, an improved approach integrating stepwise linear regression (SLR) and principal component analysis (PCA) was utilized to construct a WQImin model for an effective assessment of water quality in these estuaries. Furthermore, the absolute principal component scores-multiple linear regression (APCS-MLR) model was employed to identify and quantify the environmental drivers underlying the water quality in the estuaries. The results of WQI indicated that the water quality of the sites in the estuaries of Hulun Lake was “medium” or “poor”, both before and after the rainfall, with a general deterioration in water quality in response to the rainfall. The simplified WQImin model consisted of 5 crucial parameters (i.e., TN, TP, ammonium (NH4+-N), Tur, and permanganate index (CODMn)), and it performed well without parameter weights. Spatial differences in some water parameters among the estuaries were detected, which were attributed to the natural factors and human activities upstream. The principal environmental factors affecting the water quality in the estuaries consisted of hydrodynamic processes, internal phosphorus release, external phosphorus input, external nitrogen input, nitrification in the estuaries, and external organic input and internal organic release. Therefore, we propose basin management strategies such as limiting grazing pressure, adopting enclosed pasture, wetland restoration, optimizing water renewal cycle in Hulun Lake, and transboundary water quality management to tackle water contamination in Hulun Lake.
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