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Barriers across the complex science-policy-practice interface constrain the forms and quantities of engagement that may be necessary to connect scientific knowledge with implemented solutions to problems such as adaptation to climate change. Funding agencies have been identified as one possible driver of change, and in recent years funding programs like Future Earth have developed to intentionally foster co-produced research aimed at societal transformation. Yet, few multi-year studies have been conducted to understand how science funding program designs can influence both the practice and use of research. To contribute to this gap, this study examines applied science projects funded through the US National Oceanic and Atmospheric Administration’s National Estuarine Research Reserve System from 1998-2014. Changes in the structure of this funding program, including escalating requirements for end-user engagement, offer a natural experiment from which to explore hypotheses about the how program design influences research practice, utilization, and other impacts. Interviews of project team members, end users, and program managers (n=40) supplement content analysis of project reports (n=120) to provide a large database that is the basis for both qualitative and quantitative analysis. Results illuminate how funder mandates significantly influence the intensity of interaction between researchers and practitioners as well as affect long-term change in research cultures. When interaction intensifies, corresponding gains appear in the direct use of research results. However, throughout the assessment of this research program, many indeterminacies persist, which signal the need for improved evaluation methods for collaborative research.