Against the backdrop of intertwined natural and anthropogenic disturbances, dissolved element transport in large rivers has become a core environmental research focus. This study explored the spatiotemporal distribution of F-, As, and NO3- in the karst-dominated Wujiang River, with a focus on the overlapped impacts of vulnerable karst landforms and cascade reservoirs. Mean concentrations of the three anions were 0.49 mg/L for F-, 0.75 μg/L for As, and 2.71 mg/L for NO3- showing significant correlations with karst hydrochemical traits (e.g., TDS, Ca2+). Source analysis based on positive matrix factorization indicated the combined action of natural source and anthropogenic activities. Intense evaporation and mineral desorption drove basin-wide As-F- co-occurrence. Notably, an imbalanced higher Ca2+/HCO3- bought about the persistent supersaturation of fluorite (CaF2), presenting an apparent paradox given the observed low F- levels in aqueous solutions. The high geochemical background in supergene sediments serve as a latent F- source under hydrochemical fluctuations. On the other hand, cascade reservoirs (characterized by age and HRT) further modulated anions:NO3- dynamics were governed by a balance between retention during low-flow periods and partial removal via denitrification under hypoxic conditions, while redox shifts (evidenced by the negative correlations of As with DO/Fe) altered As mobility. Though ecological and health risks of individual contaminant were low, cumulative risks were critical in the midstream of dry seasons and the upstream of wet seasons. The study stresses integrating karst and dam impacts into anion management, which is pivotal for sustainable river governance.