The pollution of freshwater resources with crude petroleum oil is a major environmental issue in oil-producing countries. As a result, the remediation of polluted aquatic ecosystems using eco-friendly and cost-effective technology is receiving increased global attention. In this study, the ability of Azolla pinnata R. Br. to remediate petroleum-polluted freshwater was assessed. The remediation potentiality was determined by evaluating the total petroleum hydrocarbon degradation percentage (TPH%) and changes in the molecular type composition of saturated and aromatic hydrocarbon fractions. TPH% was estimated gravimetrically, and changes in the molecular type composition of saturated and aromatic fractions were measured using gas chromatography and high-performance liquid chromatography, respectively. The results reveal that A. pinnata has the potential to phytoremediate freshwater polluted with low levels (up to 0.5 g/L) of petroleum hydrocarbons (PHs). After seven days of phytoremediation, the degradation rate of total PHs was 92% in the planted treatment compared with 38% in the unplanted positive control. The highest breakdown of PHs for the normal paraffinic saturated hydrocarbon fraction occurred in the presence of A. pinnata combined with Anabena azollaea (A-A), which showed a moderate degradation capacity toward total aromatic hydrocarbons (TAHs) and total polycyclic aromatic hydrocarbons (PAHs). The results indicate that A. pinnata effectively removed C18, a saturated PH, and acenaphthene (Ace), an aromatic PH. Therefore, this study suggests that A. pinnata is a useful tool for the remediation of freshwaters contaminated with low pollution levels of crude oil.