Chemical engineering has resulted in the release of anthropogenic dissolved organic matters (ADOMs) into rivers, which can influence the dissolved organic matters (DOMs) pool, and non-neutral (N_NBC) and neutral (NBC) bacterial community assemblies. However, the interplay between DOMs, ADOMs, NBC, and N_NBC assembly in rivers is poorly investigated. Herein, we investigated the influence of ADOMs on DOM composition and further untangle the response of NBC and N_NBC assemblies to ADOMs and DOMs in urbanized rivers of the Jiulong River watershed, the largest river in southern Fujian province and the second largest in this province of China. A total of 66 samples were collected from 12 sites including 6 from a less urbanized North River and 6 from a more urbanized West River. Spectroscopy analysis, neutral community model, and network analysis techniques were employed to elucidate the interplay between ADOMs, DOMs, and microbial communities. Analysis of variance was used for the significant tests, while partial least square path model (PLS-PM) was used to evaluate the effects of ADOMs and DOMs on the diversities of N_NBC and NBC. Spectroscopy analysis reveals that ADOMs’ interaction with DOMs generates a new fluorescence component (i.e., A1 [275, 250/341 nm]). Metoprolol, Trimethoprim, and Bisphenol AF significantly increase the component’s fluorescence of protein-like substances and reduce that of humic-like substances (p < 0.01). The biological index increased to over 0.8 in most river samples treated with ADOMs. These results suggest that ADOMs significantly altered riverine DOMs and enhanced biodegradation processes. Stochastic forces drove bacterial community assemblies with a ratio of ~84% and ~ 70% in rivers with low and high urbanization, respectively. Network analysis reveals higher positive (≥70%) associations of NBC and N_NBC with ADOMs and DOMs in both rivers suggesting that ADOMs and DOMs may have more positive than negative influences on both community assemblies. PLS-PM reveals that urbanization drove the influences of ADOMs on the diversities of NBC and N_NBC, and ADOMs and DOMs significantly influenced the assumed neutral bacterial communities. These findings provide insight into the impact of ADOMs and DOMs on NBC and N_NBC in aquatic ecosystems and offer a better understanding of ecological processes in community assembly.