Sand mining is a human activity that is increasing in inland waters and has profound effects on entire aquatic ecosystems. However, current knowledge of the effects of sand mining on freshwater lake ecosystems remains limited, especially for biotic communities. Here, we investigated the responses of macroinvertebrates to indiscriminate sand mining in a large shallow lake of China. Our results indicated that sand mining significantly increased the content of suspended particulate matter, total nitrogen, total phosphorus and chlorophyll a in the water column both in the sand mining area and the area adjacent to the dredging activities. While there was significantly lower total nitrogen and the total phosphorus content of the sediment were observed in the sand mining area. In terms of benthic animals, there were reductions of the macroinvertebrate density and biomass of 89.80% and 99.54%, respectively, and there was a considerable decline of the majority of macroinvertebrate taxonomic taxa as well as biological traits observed in the sand mining area due to direct dredging-induced substrate deterioration and high turbidity water. Moreover, in the area adjacent to the dredging activities, dredging-induced high turbidity water also resulted in 28% and 79% decreases in macroinvertebrate density and biomass, respectively, with a significant decrease in the densities of Bivalvia and Polychaeta but an increase in the density of Crustacea. In terms of biological traits, species (e.g., Grandidierella sp. and Sphaerium lacustre) characterized by a small body size, short life cycle and dietary sources mainly from sediment were typically associated with the ecological condition of the indirect effects of the dredging activities. Taxa (e.g., Corbicula fluminea) with a larger body size and longer life cycle that are filter feeders should be favored by the ecological conditions of the reference sites. For biomonitoring of sand mining perturbations, a number of taxonomic and biological trait indicators were proposed in our study based on indicator value analysis, and the general applicability of trait-based indicators was highlighted. We also suggest that the biodiversity indices may be less suitable indicators of sand mining effects. Given the limited understanding of the responses of macroinvertebrates to sand mining in inland freshwaters, we believe that our results may provide important information for biomonitoring of sand mining activities and provide scientific management support to governments.