Establishing policies for controlling water pollution through discharge permits creates the basis for emission permit trading. Allocating wastewater discharge permits is a prerequisite to initiating the market. Past research has focused on designing schemes to allocate discharge permits efficiently, but these schemes have ignored differences among regions in terms of emission history. This is unfortunate, as fairness may dictate that areas that have been allowed to pollute in the past will receive fewer permits in the future. Furthermore, the spatial scales of previously proposed schemes are not practical. In this article, we proposed an information entropy improved proportional allocation method, which considers differences in GDP, population, water resources, and emission history at province spatial resolution as a new way to allocate waste water emission permits. The allocation of chemical oxygen demand (COD) among 30 provinces in China is used to illustrate the proposed discharge permit distribution mechanism. In addition, we compared the pollution distribution permits obtained from the proposed allocation scheme with allocation techniques that do not consider historical pollution and with the already established country plan. Our results showed that taking into account emission history as a factor when allocating wastewater discharge permits results in a fair distribution of economic benefits.