With the rapid urbanization of the suburbs and the resultant persistent, high-intensity management of ecosystems by humans, the health of river ecosystems is being seriously threatened, ultimately resulting in damage. In this paper, 31 sites along regional river systems in Fangshan district, Beijing, were investigated during 2016-2017. Sixteen specific evaluation indicators were classified into four aspects of river functions, viz., water environment, flood control benefit, ecological benefit, and support and utilization. The analytic hierarchy process method was used to calculate the index weight; next, the river ecosystem health evaluation index system at the county scale was constructed for Fangshan district. The results showed that, for the streams in Fangshan district, the proportion of "health and sub-health" state was 58.0% and 41.9% in terms of the functions of flood control benefit and ecological benefit, respectively. However, the proportion of "below general" state in terms of the functions of water environment and support and utilization was 71.0% and 41.9%, respectively. Overall, the health of the river ecosystems in Fangshan district was poor and barely met the general functions of the river ecosystem. Meanwhile, comparing the health of the river ecosystems, Juma and Xiaoqing rivers were far superior to Dashi and Yongding rivers. River ecological baseflow was the key factor that affected the health of the river ecosystems. Thus, the government should divert clean water from local reservoirs and other areas to restore and improve the health of the river ecosystems in Fangshan district.