Phosphorus (P) is a key nutrient in freshwater systems, often acting as the limiting nutrient. The dominant sources of P in the Jiulong River watershed (S.E. China) are anthropogenic. Dissolved and particulate P species were measured in the West (WJR) and North (NJR) rivers during the wet and dry seasons of 2018 and at their river outlets during a storm (June 2019). Sources of P pollution were characterized from mainly single source subcatchments (dry season). The Agriculture source (WJR) had a total P of 114.7 ± 13.1 μg P L−1, which was mainly dissolved inorganic P (DIP) from excess fertilizer washed from the fields. By contrast, the West Urban source (sewage effluent) was mainly particulate (POP) and dissolved organic P (DOP). The effect of reservoirs in the main NJR was to decrease total particulate P (TPP) and DIP and increase POP, due to increased sedimentation of particles and biological uptake. An increase in all P species was observed at the beginning of the storm, followed by a decrease on the rising hydrograph due to dilution. The final concentration of all P species was higher than baseflow, confirming that storms increase the P flux out of the watershed. P was initially washed off the fields during the storm, and during the falling hydrograph P increased due to interflow and other longer-term sources. The high DIN:DIP ratio confirmed the key importance of P inputs from human activities in substantially altering P sources and cycling, and hence the importance of science-based management to alleviate the eutrophication problem.