The Yungui Plateau lakes, which are characterized by a highly endemic biodiversity, have been suffering severely from anthropogenic intervention in the recent decades. Studies on the response of these biodiversity to human-mediated effects are still limited. Here, we selected the typical Lake Dianchi to investigate the correlation between macroinvertebrate spatiotemporal dynamics and human-induced eutrophication across a 2-year span (2009-2010). A total of 26 taxa were recorded, and the assemblage pattern of the macroinvertebrate community was mainly controlled by the spatiotemporal (region, season, and year) density fluctuations of some pollution-tolerant species (Limnodrilus hoffmeisteri, Tubifex tubifex, Branchiura sowerbyi, and Chironomus plumosus). Taxon richness, total density, biomass, and the abundance of Oligochaeta and Chironomidae decreased from the north to the south of the lake but were much higher in 2009 than in 2010. Moreover, the high densities of total assemblages and oligochaete occurred during spring and/or autumn, whereas that of chironomids was only high during summer. The contributions of important factors varied in different seasons, but the community variations were mainly shaped by eutrophication-related factors (e.g., Chla, N, and P). Variance partitioning analyses showed that aquatic factors were able to explain more community variations than sediment (6.9-36.6 vs. 5.3-14.7%) across seasons, but their interactive effects were negligible. The results of this study will be beneficial for restoring and managing hypereutrophic lakes in the Yungui Plateau and imply the necessity of long-term monitoring in bioassessment projects involving intensively disturbed lakes.