Increasing cases of lake eutrophication globally have raised concerns among stakeholders, and particularly in China. Evaluating the causes of eutrophication in waterways is essential for effective pollution prevention and control. Xiao Xingkai Lake is part of and connected to Xingkai (Khanka) Lake, a boundary lake between China and Russia. In this study, we investigated the spatio-temporal variabilities in water quality (i.e., dissolved oxygen (DO), total nitrogen (TN), total phosphorus (TP), chemical oxygen demand (COD_Mn) and ammonium-nitrogen (NH ⁺₄ -N)) in Xiao Xingkai Lake, from 2012 to 2014, after which a Trophic Level Index was used to evaluate trophic status, in addition to the factors influencing water quality variation in the lake. The DO, TN, TP, COD_Mn and NH ⁺₄ -N concentrations were 0.44–15.57, 0.16–5.11, 0.01–0.45, 0.16–18.31, and 0.19–0.78 mg/L, respectively. Compared to the Environmental Quality Standards for surface water (GB 3838-2002) in China, the lake transitioned to an oligotrophic status in 2013 and 2014 from a mesotrophic status in 2012, TN and TP concentrations were the key factors influencing water quality of Xiao Xingkai Lake. Non-parametric test results showed that sampling time and sites had significant effects on water quality. Water quality was worse in summer and in tourism and aquaculture areas, followed by agricultural drainage areas. Furthermore, lake water trophic status fluctuated between medium eutrophic and light eutrophic status from September 2012 to September 2014, and was negatively correlated with water level. Water quality in tourism and aquaculture sites were medium eutrophic, while in agricultural areas were light eutrophic. According to the results, high water-level fluctuations and anthropogenic activities were the key factor driving variability in physicochemical parameters associated with water quality in Xiao Xingkai Lake.