The Floristic Quality Index (FQI) is a tool used to assess the conservation value of natural areas and monitor restoration success. Each native plant species is assigned a coefficient of conservatism, a subjective rating that describes its affinity for remnant natural areas. To calculate FQI, mean coefficient of conservatism (mean C) at a site is multiplied by the square root of native species richness. However, use of FQI is sometimes problematic, mainly because it incorporates species richness, which often varies with factors other than site conservation value. We surveyed 231 wetlands in a contiguous landscape that included the Beaucoup Creek floodplain in southern Illinois, USA and investigated the influence of landscape and site characteristics on species richness, mean C, FQI, and the proportion of site floras made up by wetland species and exotic species. Species richness and FQI increased significantly with site area or perimeter, indicating a bias toward higher assessments of quality in larger areas. Species richness and FQI in emergent wetlands increased with sampling date, suggesting that these sites should only be surveyed late in the growing season. Mean C and the proportion of site flora made up by wetland species decreased with increasing inter-wetland distance, indicating that isolation affects species composition. Both decreasing area and increasing inter-wetland distance were associated with lower FQI scores. Mean C, although not completely area-independent, was less strongly correlated with sampling date or area and may provide a more robust indicator of relative site conservation value than FQI when using the metrics to evaluate conservation value of jurisdictionally delineated plant communities.