“Fee to tax” on water resource is a vital administrative means and policy in saving water priority and two hands exertion. Precise differentiated taxation quota can perform the leverage of price. This paper, viewing from the actual water resource quota in piloting areas, uses water resource values theory, economy land royalty theory and PSR model to analyze the impacts of spatial differentiation on water resource taxation quota. This paper, referring to comprehensive evaluation model of water resource, selects key indexes to establish three multiple regress models based for agriculture and special industry based on underground and surface types, and compares the factors difference on different water sources. The research indicates that water resource taxation quota is a joint aftermath of multiple elements under spatial differentiation, underground water resource taxation quota of agriculture use is largely influenced by over water use, while quota on special industry by markets's Differentiated taxation quota shall apply in areas, water sources and industries