In Finland, community water supply has increasingly relied on natural groundwater and artificially recharged groundwater as the raw water source. Several managed aquifer recharge (MAR) projects have been co-created with involved parties and have proceeded well, while some cases have raised considerable resistance among the stakeholders. It seems that success or failure in MAR cooperation is related to management cultures and the ways in which various interests are taken into account, from the very beginning and throughout the process. Empirically, this paper builds on comparison between two conflictual case studies in Finland: one in the Tampere region and the other in the Turku region. The study analyses the major constraints of these projects through the lens of collaborative rationality, also drawing upon discourse analysis and negotiation theory. The material is gathered through thematic interviews of stakeholders, newspaper articles and a stakeholder workshop. The results indicate that conventional management approaches, drawing from expert-based instrumental rationality, were insufficient in both cases. The collaborative rationality framework suggests that legitimacy for the groundwater projects should be gained through joint knowledge production and inclusive multiparty interaction for creating options for collaboration. Both cases lacked the tools and know-how for authentic dialogue and collaboration. The emerging paradigm emphasizes more collaborative approaches for natural resources management and urban planning. While MAR projects operate inside these areas and are highly complex in nature, it is essential to embrace the emerging paradigm in order to promote MAR systems along with their huge potential.