Humic acids (HA) are common mediators in redox reactions in the aquatic environment. The structures and properties of HA are greatly influenced by environmental factors such as external electrons. In this study, qualitative changes in electron-modified HA and the underlying mechanisms were reported, which not only contribute to understanding the fate of HA and their impact on organic pollutants, but could facilitate their potential use for water purification. The photochemical activity and electron-donating capacity of HA were improved due to the increase of phenolic and carboxyl components via the reduction modification by electrons, creating a novel and efficient photo-bio-electro-Fenton system mediated by HA under neutral conditions without the use of hydrogen peroxide (H2O2). The in-situ continuous production of H2O2 ensured an adequate supply of hydroxyl radicals in this coupled system, achieving mineralization (92%) of HA and 17α-ethinylestradiol (EE2), a common synthetic estrogen with high estrogenic potency. Two degradation pathways with five degradation intermediates of EE2 were identified in our study. Effluents from the coupled system showed decreased endocrine-disrupting activity. Our findings demonstrated a new approach for the in-situ modification and potential use of HA for water treatment and particularly the concurrent degradation of HA and organic pollutants through a photo-bioelectrochemical system mediated by HA.