Resumo. Abstract Aim Studies on biological communities that take into account only the species composition and abundances (or biomass) and their relative contributions, most of the time, do not reflect their ecological functions, especially considering the wide spatial and temporal variation of large shallow lakes. This paper aimed at evaluating the influence of environmental spatial and temporal heterogeneity on the functional structure of phytoplankton in a subtropical large shallow lake. Methods Seasonal samplings were carried out in 2010 and 2011, in 19 sampling sites distributed along the entire length (90 km) and width (3-10 km) of Lake Mangueira, a large (820 km2 ) and shallow lake (zmean = 2.6 m), comprising the littoral and pelagic zones of the north, central and southern regions. Abiotic variables and phytoplankton functional traits (volume, maximum linear dimension, life forms) and functional groups were analyzed as measures of functional structure. Results The results showed that there was no spatial organization of phytoplankton functional traits during the study. Colonial non-flagellated organisms, organisms with cellular volume between 103 and 104 μm3 and greater than 104 μm3, and with maximum linear dimension between 21 and 50 μm prevailed in all zones and regions. Phytoplankton functional groups and traits responded to resource variation, especially increasing their variety and contribution during spring and summer periods. Conclusions The functional structure of the phytoplankton community in Lake Mangueira, here accessed by functional traits and RFGs, was more conditioned by its environmental temporal variability rather than by the spatial variation, indicating that the resources and life conditions seasonal variation strongly influence the phytoplankton in this ecosystem.