Little is known about the trophic interactions within shallow lakes from the Mediterranean region, although there is evidence of their distinctive features compared to northern temperate shallow lakes (particularly when considering their ichthyocenosis). To address this gap, we conducted a study on the seasonal dynamics of the zooplankton community in Lake Vela (Portugal), a turbid and eutrophic shallow lake, which exhibits marked dominance of alien fish species. Lake Vela was shown to be highly productive and turbid, except during a period of higher transparency, from January to April. The increase in transparency was attributable to a rise in water level, which reduced the amount of re-suspended particles. Transparency was additionally improved by a peak in Daphnia longispina densities (February and March), which transiently reduced chlorophyll concentrations to low levels (clear water phase). In the remainder of the year, the zooplanktonic assemblage was dominated by small-sized zooplankters (mainly Bosmina and cyclopoid copepods). Daphnia were virtually absent from August to December. Regression and multivariate analyses identified seston and fish predation as the main environmental gradients shaping the zooplanktonic assemblage. During the clear water phase, competition for resources also seemed to contribute to Daphnia dynamics. The observed pattern of seasonal dynamics of the zooplankton of Lake Vela was overall concordant with the PEG model, although the timing of certain events was different, most notably the peak of Daphnia dominance and the more prolonged influence of fish, relatively to northern temperate lakes. Our results suggest that both planktivory (by alien fish) and turbidity (seston) are issues that need to be addressed if adequate restoration programs are to be implemented.