Steroidal estrogens, recognized as endocrine-disrupting compounds, pose considerable environmental hazards because of their harmful impacts on aquatic life. The persistence and fate of estrogens in water columns are largely dependent on degradation mediated by indigenous microbial consortia, which are also significantly affected by natural organic matter (NOM). The interplay between NOM and microbial communities is essential for the functioning and sustainability of water ecosystems. In this review, we synthesized current research on the occurrence, transformation, and biodegradation of estrogens in water columns using a bibliometric and systematic approach. The characteristics of NOM, including origin, concentration, and bioavailability, markedly influence estrogen biodegradation through growth promotion, co-metabolism, enzymatic stimulation, and chemical binding, which can either augment or impede biodegradation. Under anaerobic conditions, NOM can also facilitate biodegradation by serving as an electron acceptor and shuttle, with its effectiveness varying based on its redox status and environmental conditions. Moreover, estrogen biodegradation is intricately linked to the promotion of biodegradable compounds in NOM on microbial biomass, extracellular polymeric substance production, and biofilm structures. However, the interaction between NOM and extracellular microbial enzymes is dual-faceted; it can enhance their stability and activity, fostering biodegradation, or it may inhibit these processes via competitive adsorption and complexation. In addition, microbial consortia exhibit dynamic responses to fluctuations in NOM characteristics, with differing microbial entities metabolizing substrates in diverse and interactive manners. The balance between deterministic and stochastic processes in the community assembly further dictates the structure-function relationship. Higher diversity generally leads to higher biodegradation capacity when deterministic assembly dominates, but biodegradation is restricted when stochasticity dominates the assembly process. This review underscores the critical role of NOM and microbial interactions in the biodegradation of estrogens in aquatic environments and advocates for a more profound investigation into the interplay dynamics between microbes and NOM to enhance the efficacy of water-quality management and contaminant remediation strategies.