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The functioning of nesting colonies of birds can significantly affect the flora and the soil. Colony species that modify soil characteristics at their nesting sites include the Rook Corvus frugilegus. In order to assess the effect of this species on poor and fertile habitats, we analysed biogenic element concentrations and soil acidity, and investigated the taxonomic representation of plants under the nests and at control sites without nests. Two-way ANOVA showed that the habitats significantly differed in most of soil parameters. The presence of Rook colonies contributed to increased humidity and acidity of the soil and a higher biogenic element content. A varied influence of Rook colonies on plant species diversity was observed, depending on habitat type. Rook nesting caused a fall in the overall number of plant species in the poor habitats, and a corresponding rise in the fertile habitats. Rooks contributed to a rise in the mean number of ruderal species and a fall in the mean number of meadow species. A synergy between habitat type and collection site was identified in the case of ornithochorous species.