The existing regional ecological compensation policies for the water environment have deficiencies such as incomprehensive compensation factors and scope, unreasonable and inappropriate compensation standard setting, which made the policies lag behind the dynamic changes of the social economy and ecological environment. In view of these issues, the existing regional compensation method for the water environment in Changshu City, Jiangsu Province is improved. According to the requirements of regional economic development and water environment management, the administrative division is taken as the basic unit, factors such as the concentration of water quality, regional water use and sewage discharge at cross sections were considered to formulate new dynamic laddered calculation methods for water environment compensation based on the water quality category, excessive water use and excessive pollution discharge at tranboundary river sections. These methods, which are applicable to inter-regional and intra-regional contexts respectively, are designed to address current compensation issues and to make the compensation standards more scientifically grounded, so as to enhance the level and effectiveness of water environment management and foster the sustainable development of water ecosystems.