Studies of biological communities in Amazonian lakes are limited to floodplains of large rivers. However, the high-altitude lakes of the Serra dos Carajás differ from other lakes in the region due to the high natural concentration of iron and manganese. An important component of this biological community are the macroinvertebrates, some of which are sensitive to environmental and chemical variables. However, little is known about the influence of heavy metal concentrations on this community component in Amazonian lakes. In our study, we observed the importance of variables such as water depth and concentration of chemical elements in sediments on the macroinvertebrate community. Through a redundancy analysis, we found that the depth of the lake affects the number of species and the composition of the benthic macroinvertebrate community. We also found a relative importance of the concentration of manganese in the sediment for the community studied. Our results indicate that the macroinvertebrate community is differentiated in the marginal and central regions of the lake, since the deposition of organic matter and heavy metals in the sediment is different in these two regions of the lake. The relationship found has implications for the management and restoration of upland lakes in the Amazon, helping to preserve this unique ecosystem.