Phytoremediation of oil pollution using free-floating aquatic plants is a promising method for water body cleaning. In this study, the influence of Eichhornia crassipes and Pistia stratiotes on the degradation of oil pollution was investigated. The loss of oil alkanes and the rheological characteristics of water were evaluated, and an analysis of the emerging rhizospheric microbial communities was carried out using high-throughput sequencing. The presence of E. crassipes and P. stratiotes plants in oil-contaminated tanks had no effect on the degradation of oil alkanes. However, the presence of plants promoted the development of rhizospheric bacteria capable of growing in oil-contaminated environments. Alpha diversity of microbial communities in oil-contaminated samples was higher in the presence of plants. Additionally, plants significantly reduced the water/oil interfacial tension, which facilitated the availability of hydrocarbons for biodegradation. A difference was noted in the microbiome between E. crassipes and P. stratiotes. Changes in the composition of microbial communities highlight the potential of E. crassipes and P. stratiotes as rhizospheric hosts for microorganisms in the phytoremediation of water bodies.