Shenzhen, as the first special economic zone in the world, has been in the process of rapid urbanization for 30 years. Many special economic zones have been established in China and other nations following Shenzhen’s experience. However, Shenzhen has attained significant economic development with an attendant cost of environmental degradation, and similar results may be seen in other zones in the future. Here we use a pollution index method to evaluate the effect of such rapid urban development on the surface water quality in Shenzhen from 1991 to 2008. Rapid urbanization has affected surface water quality, but environmental policies can mitigate some of these effects, although such policy-induced improvements required some time before showing efficacy. As their use of special economic zones proliferates worldwide, greater consideration of the potential effects on water quality, and their overall sustainability, must receive greater attention.