Freshwater ecosystem provides a variety of services to humanity, and in return, human activities give strong stress on the services, particularly in urban area. It is of significance to study the impact of human occupation and stress on freshwater ecosystem. In this paper, a water equivalent method was used to calculate the human occupation on the freshwater ecosystem services in Beijing from 1998 to 2007, and assessed the human stress effect on the freshwater ecosystem, based on the total amount of water resources. In the past 10 years, the water equivalent of human activities in Beijing was about 5 to 17 times larger than the supply of the freshwater ecosystem. The water equivalent of the ecosystem services was decreased in the order of water environment purification > water resources supply > water habitat maintenance > water safety regulation. The gap between the consumption and the supply of freshwater ecosystem services had a trend of increasing to decreasing from 1998 to 2007, with the largest gap occurred in 1999. This study revealed that there was a huge gap between the consumption and the supply of freshwater ecosystem services in Beijing, which would inevitably result in the overloading occupation of the water resources in the City and give stress to the other regions.