The problem of institutional fit in social-ecological systems has been empirically documented and conceptually discussed for decades, yet there is a shortage of approaches to systematically and quantitatively examine the level of fit. We address this gap, focusing on spatial fit in an urban and peri-urban regional landscape. Such landscapes typically exhibit significant fragmentation of remnant habitats, which can limit critical species dispersal. This may have detrimental effects on species persistence and ecosystem functioning if land use is planned without consideration of the spatial patterns of fragmentation. Managing habitat fragmentation is particularly challenging when the scale of fragmentation reaches beyond the control of single managers, thereby requiring different actors to coordinate their activities to address the problem at the appropriate scale. We present a research approach that maps patterns of collaborations between actors who manage different parts of a landscape, and then relates these patterns to structures of ecological connectivity. We applied our approach to evaluate the fit between a collaborative wetland management network comprising all 26 municipalities in the Stockholm County in Sweden and an ecologically defined network of dispersed but ecologically interconnected wetlands. Many wetlands in this landscape are either intersected by the boundary between two or more municipalities, or are located close to such boundaries, which implies a degree of ecological interconnectedness and a need for intermunicipal coordination related to wetland management across boundaries. We first estimated the level of ecological connectivity between wetlands in neighboring municipalities, and then used this estimate to elaborate the level of social-ecological fit vis-à-vis intermunicipal collaboration. We found that the level of fit was generally weak. Also, we identified critical misalignments of ecological connectivity and intermunicipal collaboration, respectively, as well as collaborations that represented an adequate alignment. These findings inform on where to most effectively allocate limited resources of collaborative capacity to enhance the level of social-ecological fit. Our approach and results are illustrated using maps, which facilitates the potential application of this method in land use planning practice.