A method and apparatus is provided for the continuous microbial remediation of organic wastes in sewers and other waste-laden environments utilizing in-situ microbial seeding. A bio-reactor containing inoculated carrier media is suspended within a sewer wet-well or other similar environment, and is at least partially immersed in the waste-laden fluid to be treated. Air and nutrients are continuously supplied to the bio-reactor via conduit from a remote, easily accessible location. Beneficial microbial populations are permitted to thrive and spread throughout the waste-laden environment, mineralizing organic wastes and eventually becoming dominant within the subject environment.