Contamination by oil spills in coastal ecosystems, especially in mangrove zones, has been common in countries with oil industry. The aim of this study was, therefore, to evaluate the efficiency of application of the two biotechnologies developed for pilot-scale remediation with hybrid bioreactor, using intrinsic bioremediation (indigenous microorganisms), and phytoremediation (Avicennia schaueriana and Rizophora mangle). The results showed greater degradation of the saturated hydrocarbons in the units receiving a nitrogen–phosphorus–potassium (NPK) fertilizer blend, indicating the better biostimulation efficacy of this fertilizer. The bioaugmentation experiment indicates that the consortiums showed promise for use in bioremediation: they increased the degradation by approximately 30%. Greater efficacy in removing organic compounds from sediments was observed in two phytoremediation models (approximately 89% removal). The three models were effective in the removal of fraction 3A (C16-23), but the two phytoremediation models achieved much greater degradation of fractions 3B (C23-34) and 4 (C34-40). The data indicate that the two phytoremediation models were more effective than the intrinsic bioremediation model in the degradation of petroleum hydrocarbons.The results suggest that the phytoremediation model, through its various mechanisms, may become a technique for the removal of petroleum hydrocarbons in the presence of metals in industrial areas.