A new and improved in situ biogeochemical reactor, methods for constructing such reactors, and methods for using such reactors, for biodegradation, detoxification and mineralization of toxic organic and inorganic compounds, especially dioxins, in contaminated geologic settings, such as waterways is disclosed. The system includes both an anaerobic component and an aerobic component that are coupled to each other. The system is enriched with carbon, nutrients and growth factors in sufficient amounts to establish a full spectrum oxidation-reduction gradient thereby enabling, promoting and providing indigenous microbial populations to biodegrade, detoxify, and mineralize toxic organic and inorganic compounds in a contaminated geological site.