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The water environment restoration project portfolio (WERP) selection is discussed in this paper. By complying with the analysis of the project’s multidimensional property and operation mode, this paper develops the chance constraint and the management constraint of the WERP from the perspectives of public service and enterprise operation. In addition, the multi-objective mixed integer linear programming model is constructed by combining the expectation method and the fuzzy chance constraint programming method. The results demonstrate that: (1) Our proposed method successfully circumvents the occurrence of local objective optimization within a specific confidence interval, thereby achieving a balance between economic and water environment restoration objectives; (2) including fuzzy chance constraints in our proposed method significantly diminishes the risk of exceeding the WERP capacity, thereby ensuring the effectiveness of water environment restoration by adopting a market-based approach. However, further examination of the impact of various sub-projects in WERP is necessary, along with the integration of novel evolutionary algorithms to enhance the efficiency of our model.