Atrazine (ATR) is an endocrine disruptor known for its persistence and mobility. While the diffuse characteristics and potential risks of ATR have been extensively studied, its transregional migration and degradation characteristics have received less attention. In this study, a modified mass balance approach considering the diffuse source (DS), tributaries, water resource usage, degradation, adsorption, and evaporation was developed based on the traditional mass balance framework and field sampling to estimate the DS fluxes of ATR in a large river basin. Field sampling revealed that the ATR concentration in the surface water increased downstream, whereas the ATR levels in suspended particulate matter decreased. The ATR degradation ratio also decreased downstream, suggesting increased input along the river. The modified mass balance approach identified DS as the primary ATR source in the river, followed by tributaries. Together, the DS input and tributary inflow accounted for 95.6 % ± 2.1 % of the total ATR flux, with DS alone contributing 73.8 % ± 10.2 %. Finally, the ATR parent and its hazardous materials (ATR, desethylatrazine, and desisopropylatrazine) accounted for 6 % and 27 %, respectively, of the total ATR content that reached the estuary. This integrated consideration of ATR and its degradation products offer a new perspective on their transregional migration and degradation patterns resulting from diffuse pollution.