The effectiveness of in situ bioremediation can be affected by an insufficient understanding of high site/soil heterogeneity, especially in cocontaminated soils and sediments. In this study, samples from multiple locations within a relatively small area (20 x 20 m2) contaminated with benzene, toluene, ethylbenzene, and xylene (BTEX) and chlorinated aliphatic hydrocarbons (CAHs) were compared to examine their physicochemical and microbial properties. Unsupervised clustering analysis of 16S rRNA gene amplicon and metagenome shotgun sequencing data indicates that the indigenous community differentiated into three distinct patterns. In Cluster 1, Pseudomonas, with multiple monooxygenases and glutathione S-transferase (GST), was enriched in samples contaminated with high concentrations of BTEX and CAHs. Cluster 2 contained a high fraction of cometabolic degraders. Cluster 3 was dominated by Ralstonia and organohalide-respiring bacteria (OHRBs) mediating the reductive dechlorination of CAHs. Significant differences in composition and function among microbiomes were attributed to the differential distribution of organic pollutants, even in such a small area. Incorporating genomic features with physicochemical data can significantly enhance the understanding of the heterogeneities in soil and their impacts on microbial communities, thereby providing valuable information for the optimization of bioremediation strategies.