Co-design processes are of key importance in planning and implementing Nature-based Solutions (NBS), but require boundary management between diverse holders of local, practical and scientific knowledge. Participatory and map-based planning tools, such as Geodesign workshops, can facilitate such boundary management through mobilising knowledge holders, and translating and negotiating between different perspectives. The COVID-19 pandemic hindered physical mobility, but offered an, albeit unintended, opportunity to explore new ways of virtual mobility for facilitating boundary management in NBS co-design through digital participatory tools. This short communication aims to demonstrate how a spatial planning process for NBS can be facilitated in an online context. We draw on an international case study for co-designing NBS in Costa Rica, conducted during the severe lock-down restriction of the COVID-19 pandemic. This novel approach showcases how physical presence and movement is replaced by virtual mobility enabled through an online geographic map-based environment that allowed participants to communicate their opinions and co-create local and regional NBS actions. The case study included developing and testing a co-design tool to understand and map local perceptions of social-ecological problems, and an actual co-design process for siting NBS options and jointly exploring their implications. We present two levels of the process: 1) the adaptation of the co-design tool, and 2) the use and usefulness of the co-design tool. Our evaluation shows that the tool served its purpose well and provided useful support to local stakeholders. We recommend to test further strategical combinations of in-person and virtual methods in NBS co-design processes to improve NBS planning and implementation.