Riverine floodplains are ecologically remarkable systems that have historically faced strong anthropogenic pressures. The aim of this study was to examine whether the phytoplankton functional approach by Reynolds is a useful tool for disentangling anthropogenic pressure from the impact of natural flooding on a riverine floodplain lake. Lake Sakadaš, part of the large conserved river–floodplain system along the Danube River (Kopački Rit, Croatia), was used as a case study. Historical data on phytoplankton dynamics from the 1970s, when the lake was exposed to direct inflows of agricultural wastewater, were compared with current data from a time when the lake was a strongly protected area. Analysis of the phytoplankton community, based on functional groups and their beta diversities, revealed clear variation between the observed periods. The heavy bloom of species from only one functional group with extremely high biomass indicated a highly impacted environment in the past. Recent data suggest that, with the cessation of direct pollution, near-natural hydrological conditions with flooding as a fundamental environmental driving factor, support algal assemblages characteristic of a naturally eutrophic lake. Assessing multiple pressures on floodplain lakes and disentangling their specific impacts on ecological statuses are crucial for defining the protection and sustainable management of these particularly sensitive and endangered freshwater systems.