The conservation and sustainable management of the marine environment requires knowledge exchange among scientists and decision-makers to enable learning and support evidence-based decision-making. Efforts to improve knowledge exchange have often been hindered by a paucity of empirically-grounded guidance to help scientists and practitioners implement research programs that actively facilitate knowledge exchange. To address this, we evaluated the Ningaloo Research Program (NRP), which was designed to generate new scientific knowledge to support evidence-based decisions about the management of the Ningaloo Marine Park in north-western Australia. Specifically, we evaluated (1) program outcomes, including the extent to which new knowledge informed management decisions; (2) the barriers that prevented knowledge exchange among scientists and managers; (3) the key requirements for improving knowledge exchange processes in the future; and (4) the core capacities that are required to support knowledge exchange processes. We found that while the NRP generated expansive and diverse science outputs directly relevant to the management of the Ningaloo Marine Park, very little has been integrated into decision-making processes. Based on our findings we identify a set of principles that should be implemented as part of any applied research program, including; (i) stakeholder mapping prior to the commencement of research programs to identify all stakeholders, (ii) research questions to be co-developed by all stakeholders, (iii) implementation of participatory research approaches, (iv) use of a knowledge broker, and (v) tailored knowledge management systems. We also identify the key individual, institutional and financial capacities that must be developed to underpin successful knowledge exchange strategies.