Contamination of soil and water with petroleum hydrocarbons has significantly increased as a result of accidental spills, thus, several biological systems have been applied to cleanup and rehabilitate the negatively impacted regions. The present review discusses the fundamental principles required to understand the effectiveness of some bioremediation systems applied to soil and water contaminated with petroleum hydrocarbons and other organic pollutants. The practical aspects of several experimental approaches such as composting and soil amendment application, plant utilization and rhizosphere microbial activity as a keystone during phytoremediation, slurry bioreactors utilization, and potential utilization of microalgae to decontaminate wastewater, are also described.