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Abstract Shallow lowland lakes are critical components of the water cycle, providing an essential service function. However, the impacts of microcystin from phytoplankton communities on benthic macroinvertebrate community diversity and structure have seldom been investigated. During 2008-2012, the impacts of water environmental variables on the diversity of macrobenthic communities, including water temperature, pH, dissolved oxygen, transparency, conductivity, the permanganate index, Chlorophyll a, total phosphorus, total nitrogen, and microcystin-LR (L for leucine and R for arginine), were measured in a typical shallow lowland lake, Ge Lake. The results of the present study demonstrated that there were 31 benthic macroinvertebrate taxa in Ge Lake, including 7 oligochaetes, 7 Mollusca, 14 chironomids, and 3 other taxa. Among the macrobenthic taxa in the benthic community, opportunistic taxa such as Limnodrilus hoffmeisteri are present and can occur at greater densities in disturbed habitats. However, a significant reduction/disappearance of sensitive and clean taxa was observed among the benthic macroinvertebrates. Water temperature, dissolved oxygen, conductivity, ammonia nitrogen, transparency and total phosphorus were the main environmental variables influencing macrobenthic community structure, while water temperature, conductivity, ammonia nitrogen, Chlorophyll a, the permanganate index, total phosphorus and total nitrogen were the main factors that influenced macrobenthic community diversity indices (the numbers of taxa, Shannon’s diversity index, Margalef’s richness index, and Pielou’s evenness index). Our results underscore the severity of the effects of human activity on Ge Lake and strongly suggest that restoring the benthic invertebrate community to previous conditions would require the control and reduction of environmental pollutants and nutrients in Ge Lake.