The ecological effectiveness and success of river restoration strongly depend on the resources invested in planning. Unfortunately, this trend of restoration engineering is frequently compromised by the application of qualitative assessment and resource intensive adaptive management processes. Habitat simulation models are effective tools for selecting ecologically effective restoration measures as part of the Environmental Benefits Analysis. Through the support from a mesohabitat simulation model, we identified three habitat metrics: (1) Habitat Quantity Deficiency; (2) Alteration of Habitat Structure; and (3) Habitat Stress Days Alteration to quantify and visualize differences between restoration options in Restoration Alternatives Assessment diagram. This concept of quantifying habitat models is supported by an example of application in the Wekepeke Brook in Massachusetts, in which the habitat metrics were used to define quantitative benchmarks, goals and targets to guide the restoration process from the design to the evaluation phase. The three habitat metrics are a cost effective alternative for evaluating the ecological benefits of a planned action. The methodology contributes to a high potential for designing and monitoring restoration projects. Copyright © 2012 John Wiley & Sons, Ltd.