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A limnological investigation involving physical, chemical and biological aspects was undertaken in five tropical upland lakes (Violao − Vl, Amendoim − Am, and Tres Irmas − TI1, TI2 and TI3) from Serra dos Carajas, Brazil. Results show that these lakes are shallow, weakly stratified, and of polymictic type. These characteristics may have caused vertical mixing of limnological parameters. Seasonal changes were minor for most parameters, except for chlorophyll-a (Chl-a ) and cyanobacteria, which also showed considerable variation between lakes. In general, waters of these lakes were mostly acidic in nature (avg. pH 4.9–5.9), with high total Fe (up to 1.52 mg/L) and low electrolytic conductivity (avg. 8.13–14 μS/cm) and total phosphorus (TP) (avg. 10–35.5 μg/L). Although the water bodies have good quality and classified as class I and II types according to CONAMA Resolution No. 357/05, trophic state index (TSI) varies from ultra-oligotrophic to eutrophic state, with higher trophic state observed for Vl, TI1 and TI2. Limnological characteristics of these lakes is highly influenced by lithological and morphological parameters. Principal component analysis (PCA) reveals that Chl-a and cyanobacteria are not solely influenced by TP and lower concentrations of all these parameters in Am lake are probably due to specificities of its catchment lithology. Phytoplankton taxa in the lakes are characterized by small chroococcales groups and desmids together with filamentous algae, more commonly observed in the dry season. The zooplankton community in the lakes is mainly dominated by rotifers, followed by cladocerans and copepods. Regarding species richness, zooplankton was highest in Vl, while phytoplankton is highest in TI1, and this aspect is most likely related to lake water levels.