The phytoplankton functional group (FG) classification system sensu Reynolds enables evaluating the ecological status of rivers using the Q(r) compositional index. Here, we apply the Q(r) index to analyze the ecological conditions of the Southern Bug River, at the entire river length, in the early 20th century, testing it first on historic river phytoplankton data. Moreover, we combined the FG approach with the saprobic index and taxonomic richness to assess the ecological status of the river more reliably. The Bray–Curtis Similarity index highlighted the spatial clustering of river sites that corresponded well to the bioregions of the Eastern Lowlands and the Pontian Province. The Q(r) index revealed a higher variation in ecological status among sites than the saprobic index. Therefore, we argue that the FG approach provides a sensitive ecological status indication approach for river phytoplankton, including historical human impacts. The method may improve understanding of reference conditions and assessing the ecological status of Ukrainian rivers, as requested by the European Water Framework Directive.