Based on the one-dimension model for water environmental capacity (WEC) in river, a new model for the WEC estimation in river-reservoir system was developed in drinking water source conservation area (DWSCA). In the new model, the concept was introduced that the water quality target of the rivers in DWSCA was determined by the water quality demand of reservoir for drinking water source. It implied that the WEC of the reservoir could be used as the water quality control target at the reach-end of the upstream rivers in DWSCA so that the problems for WEC estimation might be avoided that the differences of the standards for a water quality control target between in river and in reservoir, such as the criterions differences for total phosphorus (TP)/total nitrogen (TN) between in reservoir and in river according to the National Surface Water Quality Standard of China (GB 3838-2002), and the difference of designed hydrology conditions for WEC estimation between in reservoir and in river. The new model described the quantitative relationship between the WEC of drinking water source and of the river, and it factually expressed the continuity and interplay of these low water areas. As a case study, WEC for the rivers in DWSCA of Laohutan reservoir located in southeast China was estimated using the new model. Results indicated that the WEC for TN and TP was 65.05 t x a(-1) and 5.05 t x a(-1) in the rivers of the DWSCA, respectively. According to the WEC of Laohutan reservoir and current TN and TP quantity that entered into the rivers, about 33.86 t x a(-1) of current TN quantity should be reduced in the DWSCA, while there was 2.23 t x a(-1) of residual WEC of TP in the rivers. The modeling method was also widely applicable for the continuous water bodies with different water quality targets, especially for the situation of higher water quality control target in downstream water body than that in upstream.