In this exploratory study, naturally occurring Salvinia biloba Raddi specimens were assessed for atrazine and carbendazim polluted water remediation. Experiments were carried out over 21 days in glass vessels containing deionized water artificially contaminated with 0, 5, 10, and 20 mg L−1 of atrazine or carbendazim. Atrazine had a pronounced detrimental impact on S. biloba, as no biomass development was observed in all macrophytes exposed to this herbicide in the entire concentration range. However, carbendazim-treated plants were able to grow and survive in the polluted medium even when subjected to the highest concentration of this fungicide (i.e., 20 mg L−1). In addition, increased chlorosis and necrosis were also detected in plants subjected to carbendazim as a result of the high phytotoxicity caused by atrazine. A maximal removal efficiency of ~ 30% was observed for both pesticides at 5 mg L−1 and decreased with increasing concentrations of the pollutants. The spectrum of the FTIR-ATR analysis revealed the existence of various functional groups (e.g., amide, carboxyl, hydroxyl, phosphate, sulfate) on the plants, which could be related to pesticide biosorption. In addition, at the end of the 21-day assay, seven carbendazim-resistant bacteria could be isolated from the roots of fungicide-treated plants. Therefore, the use of autochthonous free-floating S. biloba macrophytes for phytoremediation of aquatic environments contaminated with carbendazim shows great promise. Still, additional research is required to further elucidate the plant-mediated carbendazim elimination process and the role of the herbicide-resistant bacteria, and seek alternative species capable of mitigating atrazine contamination.