This study aimed at analyzing the environmental factors which determine the structure and dynamic of phytoplankton in a shallow reservoir with abundant macrophyte flora, Ninféias Pond (Brazil). It is hypothesized that, although its shallowness, periodic stratifications play an important role on its phytoplankton community. Water samples were collected monthly, from January to December 1997, in four depths (sub-surface, 1 m, 2 m, and bottom) of pelagic zone (Zmax = 3.6 m). Community seasonal and vertical variations followed a hot-rainy season with water column stratification (phase 1; Q index: medium), alternating with a cool-dry season with water column mixing (phase 2: Q index: excellent). Nanoplanktonic flagellates dominated, mainly mixotrophic species. During phase 1, Chlamydomonas sp. (G) was the main species, dominating at the anoxic and nutrient-rich hypolimnion. At the same time, richness and diversity were relatively lower. During phase 2, lower water temperatures and higher dissolved oxygen concentrations favoured the prymnesiophyte Chrysochromulina cf. breviturrita (X2). Sequence of functional groups over phases 1 and 2 was: phase 1 = G → transition = Y/P/E/D/F/W2/X3 → phase 2 = X2/Lo/X1; most of these groups have been associated to oligo-mesotrophic systems. Seasonal stratifications played a decisive role in determining the structure and dynamic of phytoplankton in the Ninféias Pond. However, in such a complex and heterogeneous system, other compartments of the food web (macrophytes, zooplankton, fishes) may also act as relevant driving forces, in synergy with the physical and chemical environment.