Microbial communities in aquatic systems are dominant drivers of chemical transformation, including contaminants of emerging concern (CECs). This study quantified shifts in microbial communities and their relationship to shifts in chemical composition in surface waters in the Willamette Valley, Oregon. In addition to bulk chemical composition shifts, the relationship between microbial communities and the concentration reduction of 8 CECs (herbicides, insecticides, pharmaceuticals) was investigated. Microbial communities were classified using 16S rRNA sequencing, and all chemicals were identified using high resolution time-of-flight mass spectrometry. Using similarity metrics to quantify shifts between samples, microbial community dissimilarity was used as a variable to explain total organic chemical community shifts. Microbial community shift potentially explained holistic chemical community shift. Identifying microbial communities that relate to relatively large chemical transformation is useful for selecting core microbial species for augmenting wastewater treatment plant bacteria to remove CECs.