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Browning of surface waters, also known as brownification, is a process of decreasing water transparency, particularly in boreal lakes surrounded by intensively managed forests and wetlands. In this paper, we review the ecological consequences and ecosystem-based management (EBM) of browning through a systematic review approach and adopt an interdisciplinary approach to formulating new governance of this complex phenomenon. To understand the effects of browning on the recreational value of freshwaters, we present primary survey data on public perceptions of recreational fishing tourists on water quality in Finland. We identify a need to develop EBM beyond the EU's Water Framework Directive (WFD) to fully account for the extensive implications of browning. We also highlight the need for a better understanding of the within-lake microbial processes to estimate the browning-associated changes in the greenhouse gas balance of lakes. Tourist perceptions of the quality of waterbodies in Finland were largely in agreement with the general proportion of waterbodies classified in a good or excellent ecological status class, but these perceptions may be detached from biological quality assessment criteria. Consequently, we suggest that the EBM of inland waters should improve the utilization of information on not only biogeochemical processes but also users' perspectives on aquatic ecosystems beyond the EU WFD., (© 2023 The Authors. Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)