Two rivers from Taiwan with different source inputs, the Danshuei (polluted) and Liwu (non-polluted), were selected to study the behavior of molybdenum (Mo) isotopes during weathering and riverine transport. In the Danshuei River, δ98/95Mo ranges from 0.83‰ to 1.50‰ (wet season) and 0.54‰ to 1.25‰ (dry season). With a few exceptions, δ98/95Mo in the Danshuei River is lighter during the wet season, while, in contrast, heavier in the dry season. In the Liwu River, δ98/95Mo varies from 0.54‰ to 1.30‰ and gets heavier along the mainstream. Using the MixSIAR model, three Mo sources are identified in the Danshuei River: seawater intrusion, rock–water interaction, and anthropogenic inputs. Seawater intrusion can explain the heavy δ98/95Mo downstream signal during the wet season contributing 14–39% from the MixSIAR model. However, the lighter δ98/95Mo signal during the dry season is most likely due to anthropogenic inputs in the middle and lower reaches of the Danshuei River contributing 75–98%. In the Liwu River, dissolved Mo isotopes correlate with SO42−/Na and (Sr/Na) ×1000 ratio, suggesting that pyrite oxidation coupled with carbonate weathering governs the heavy δ98/95Mo signature, with sequestration of light δ98/95Mo into secondary mineral phases in bedload sediments. Furthermore, these results have important implications for riverine Mo sources to the ocean, controlled by anthropogenic activity and weathering processes.