The growing extent of contaminated soil and water due to industrialization is a major global concern and the remediation of contaminated sites is a key sustainability goal. Organophosphate (OP) compounds represent a major environmental contaminant due to their role as a nerve agent and widespread application as pesticides. In addition to acute toxicity to humans, which results in over a million poisonings annually, chronic exposure to these compounds may lead to long term neurological and developmental effects. Microbial bioremediation of toxic compounds often suffers from a lack of understanding of the types and roles of degrading bacteria within the context of the diverse community and ecological drivers present in the system. New genomic technologies are leading to a more holistic understanding which synthesizes information regarding the organisms present, functional gene abundances and environmental variables. Using OP compounds as an example, we applied ecogenomic approaches and network analysis to link key taxa to OP degrading genes within a wider metabolic network to elucidate the consequences of organophosphate pesticide contamination on microbial function and degradation capability in Agricultural soils. Our results demonstrated the legacy effect of OP contamination on microbial community composition and functional capability and provide a framework in which to apply system-wide tools understand processes of microbial adaptation to toxic compounds and degradation potential.