Based on the runoff, the chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) data in the Maolingjiang River Estuary section from 2014 to 2020, the inflow fluxes of COD, TN and TP were calculated by the LOADEST model. Results showed that: (1) The regression equation of COD, TN and TP fluxes into the sea from the Maolingjiang River was well fitted by the LOADEST model, there were consistencies between the simulated and measured values. (2) The simulated multi-year average COD, TN and TP inflow fluxes were 34 537 t/a, 3 302 t/a and 235 t/a, and the monthly average inflow fluxes were 2 878 t/month, 275 t/month and 19.58 t/month, respectively. COD, TN and TP inflow fluxes in the wet season accounted for 77%, 80% and 71% of the total annual inflow fluxes, respectively. The multi-year average inflow fluxes of COD, TN and TP were 21 059~25 271 t/a, 1 775~2 130 t/a and 70~84 t/a from non-point sources, respectively. COD and TN were mainly controlled by non-point sources. TP was controlled not only by non-point sources but also by point sources. (3) Comparatively, the multi-year average inflow fluxes of COD, TN and TP of the Qinjiang River were about 1.16, 2.15 and 2.37 times those of the Maolingjiang River, respectively. The difference of inflow fluxes of COD, TN and TP from the Qinjiang River and Maolingjiang River were mainly affected by the number of people living along the river.