Lake Xingyun is a hypertrophic shallow lake on the Yunnan Plateau of China. Its water quality (WQ) has degraded severely during the past three decades with catchment development. To better understand the external nutrient loading impacts on WQ, we measured nutrient concentrations in the main tributaries during January 2010–April 2018 and modelled the monthly volume of all the tributaries for the same period. The results show annual inputs of total nitrogen (TN) had higher variability than total phosphorus (TP). The multi-year average load was 183.8 t/year for TN and 23.3 t/year for TP during 2010–2017. The average TN and TP loads for 2010–2017 were 36.6% higher and 63.8% lower, respectively, compared with observations in 1999. The seasonal patterns of TN and TP external loading showed some similarity, with the highest loading during the wet season and the lowest during the dry season. Loads in spring, summer, autumn, winter, and the wet season (May–October) accounted for 14.2%, 48.8%, 30.3%, 6.7%, and 84.9% of the annual TN load and 14.1%, 49.8%, 28.1%, 8%, and 84.0% of the annual TP load during 2010–2017. In-lake TN and TP concentrations followed a pattern similar to the external loading. The poor correlation between in-lake nutrient concentrations and tributary nutrient inputs at monthly and annual time scales suggests both external loading and internal loading were contributing to the lake eutrophication. Although effective lake restoration will require reducing nutrient losses from catchment agriculture, there may be a need to address a reduction of internal loads through sediment dredging or capping, geochemical engineering, or other effective measures. In addition, the method of producing monthly tributary inflows based on rainfall data in this paper might be useful for estimating runoff at other lakes.