An integrated floristic and palynological approach was carried out at the site of national interest “Laghi di Mantova e Polo Chimico” to obtain an environmental assessment useful for monitoring polluted sites. The flora of highly contaminated sectors (area A and area B) was surveyed, and the floristic composition and ecological strategies of the species were compared with a control sector (area C). A total of 195 species were observed in the three sectors. Pollen preservation of six selected species was checked as a bioindicator of environmental health in the same sectors. Area A and area B likely share similar environmental pressures, including anthropogenic stressors such as pollution, geographical proximity and a similar set of habitats, leading to similarities in flora composition. Similarly, the incidence of pollen without cytoplasm is higher in area A (9.3%) and area B (7.6%) than in area C (2.5%). The floristic differences among the sectors and the quantity of empty or abnormal pollen, together with the CSR strategies adopted by the species, suggest that the effects of anthropogenic impact on local vegetation can be detected at both macroscopic and microscopic levels. The discovery of the protected species Narcissus pseudonarcissus in area C is noteworthy, which may be important in directing efforts towards the protection of plant communities in this sector.