Protection areas favor diversity as they decrease the impact of anthropic disturbance on biological communities. Testing its effects on diverse biological communities is a pivotal step to understand how different trophic levels react to such management and conservation strategies. Here, we used data collected from 1993 to 2018 from a subtropical floodplain to evaluate the effect of the installation of a protection zone on the taxonomic and functional diversity of the phytoplankton community. We showed that the installation of the park had a positive effect on the aquatic community, mainly related to the decrease of cyanobacteria dominance and to the increase of phytoplankton functional groups. However, our results also suggested that dynamics occurring in a scale beyond the park seemed to influence key factors for the phytoplankton community, such as transparency and nutrient concentrations. Thus, although we showed that a compensatory measure had a positive effect on biodiversity, we believe that the establishment of protection zones must also consider and integrate the management of the river basin where the areas to be protected are located.