One of the most influential environmental laws in the US – the 1972 Clean Water Act – included the visionary objective of maintaining and restoring aquatic ecological integrity. However, the efficacy of the Act depends on how integrity is assessed. Reviewing the assessment literature for fresh waters over the past 40 years, we found evidence of methodological trends toward increased repeatability, transferability, and robustness of assessments over time. However, implementation gaps were revealed, based on the relatively weak linkages to freshwater policies, stakeholder involvement, emerging threats, and conservation opportunities. A related survey of assessment practitioners underscored the disparity between need versus availability of assessments that guide management policies. Technological changes in data collection and synthesis have clearly influenced assessments, and appear to have led to a reduced reliance on ecological response indicators and corresponding increases in stressor-based metrics. We recommend designing assessments around specific freshwater policies and regulations to improve applicability of assessment products for management and conservation.