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The present study demonstrates the effects of abiotic variables on phytoplankton in two different tropical climates. Samples were taken from tropical reservoirs, including six from a tropical climate (As) and five from a semi-arid climate (BSh). Phytoplankton samples were identified, biomass was quantified and climatic and physicochemical variables were evaluated. Canonical analyses were performed in order to observe the effects of abiotic variables on phytoplankton. In both As and BSh ecosystems, the effects of the physicochemical variables were significant, but the synergistic effects between variables and climatic conditions were more pronounced in BSh. Micronutrients had a significant role in structuring the phytoplankton community in both As and BSh. In As, Cylindrospermopsis raciborskii occurred in the presence of lower concentrations of zinc and copper, whereas in BSh this species was present in the presence of higher concentrations of zinc. In the As climate, Geitlerinema amphibium, Cyclotella meneghiniana, Planktothrix agardhii and Microcystis aeruginosa were associated with higher sodium concentrations in the water, whereas in the BSh climate these species experienced lower rainfall. The findings of the present study show that climate determines the effects of abiotic variables on the phytoplankton community in both an independent and synergistic manner. In the present study, phytoplankton in tropical and semi-arid reservoirs is mostly regulated by nutrients, the effects of which vary according to climate.