The general objective for this paper is to reveal the dynamic relationships between the rapid economic development, water pollution and the subsequent waste-load allocation in different economic sectors through a case-study in Shenzhen City, South China. Two-objective analysis model was employed based on the input-output table for Shenzhen with the full consideration of various constraints in local area. The improved Tchebycheff procedure was used for obtaining the solutions. The predictions were made on economic development and pollutants from wastewater in different sectors and different planning years. The present study allows for the consideration of the economic structural adjustment. It is found that the current situation of economic structure is generally good and is subject to further adjustment in Shenzhen, although it has undergone the rapid development in the past 18 years. When the maximum Gross Domestic Production and the minimum Chemical Oxygen Demand are chosen as the two objectives subject to other constraints, the harmonized results indicated a scheme that claims substantial reduction of polluting effluences in Shenzhen while closely keeping the economic growth rate as planned.