Environmental justice sheds light on the distributive and procedural aspects of planning and decision-making. We examined the challenges arising from the perspective of environmental justice on multi-level and participatory environmental governance by exploring the governance of aquatic environments in the Helsinki Metropolitan Area. We found three main challenges and potential responses to them. First, even though most of Helsinki’s shoreline is free and/or accessible by road and accordingly used actively by people for recreational purposes, many parts of the shoreline are perceived as inaccessible, reflecting a need to combine factual and perceived accessibility of aquatic environments in detail during the planning processes and to discuss reasons for possible discrepancies between these two. Second, there was a remarkable seasonal variation in the use of aquatic environments, so more attention should be paid to social-demographic factors explaining the distribution of the use of urban nature. Third, it seems to be difficult to capture the variety of perceptions of people and to integrate them into planning and decision-making processes even on a local scale, and this challenge is likely even more pronounced on higher levels of planning and governance. Thus, better integration of regional and local-scale planning procedures should be encouraged. Building on these observations, we conclude that integration of procedural and distributive environmental justice into the practices of the governance of aquatic environments could remarkably decrease unwanted trade-offs and potential conflicts in their use and management.