The success of numerous Federal natural resource conservation programs to meet output objectives (acres of wetland restored) has been well publicized. However, a failure to tie project-based outputs to outcome-based goals (increase in duck population), has left bureaucrats scrambling to justify budget increases to a Congress that demands accountability as evidenced by sound science. This failure results from policy directives that do not outline assessment criteria within programs that can successfully identify a collective outcome based on a series of outputs. New policies must contain assessment criteria sufficient in detail to drive prioritization of individual projects, be cost effective, be applicable on a national scale, and provide information that determines the project(s) contribution toward the national goals. In 2006 five pilot Fish Habitat Partnerships received initial funding through the recently established National Fish Habitat Action Plan (NFHAP). Policy decisions are currently being made to guide these partnerships in meeting national aquatic species population goals. We address the assessment pitfalls to which past conservation programs have succumbed and outline specific policy directives that can drive NFHAP at the regional and local level. These directives will address 1) development of adequate project ranking criteria that strategically contribute specific habitat restoration outputs to achieve the desired regional population outcomes; 2) development of a Success Assessment Index that will guide implementers in determining the correct level of evaluation needed to identify progress in meeting program outcomes, and 3) guidelines for determining project specific restoration methodologies.