Planning nature conservation areas is a crucial aspect of spatial planning, shaping the overall spatial development strategy. However, significant challenges remain, particularly in forecasting, planning, and designing new conservation facilities and ecological networks. Special attention must be given to restoring small rivers to preserve water resources and protect their multifunctional riparian zones. When effectively planned, these zones can serve as key elements of ecological networks, enhancing geodiversity and biodiversity conservation while also functioning as landscape-recreational areas, geotourism routes, leisure spaces, and venues for sports activities. Conservation efforts in small river basins should begin with scientific research on the river basin’s natural characteristics and its response to anthropogenic pressures. Such research forms the foundation for developing a nature conservation strategy for territorial communities, including restoring natural river channels, legally protecting riparian zones, and establishing sustainable water use and management systems. This article examines the specific features of spatial planning for nature conservation areas, using the Kolomyika River restoration project as a case study. The Kolomyika River, a left tributary of the Prut River, was the focus of a project developed in collaboration with students as part of the academic courses “Spatial Planning of Nature Conservation Areas” and “Eco-Project Management” within the Department of Earth Sciences and Geomorphology at the Faculty of Geography, Taras Shevchenko National University of Kyiv. The project also involved researchers from the Faculty of Geography at Ivan Franko National University of Lviv and the Department of Landscape Studies at the Institute of Geography of the National Academy of Sciences of Ukraine. The research methodology integrates theoretical and regulatory sources on nature conservation activities and international best practices for restoring small rivers. The methodological recommendations presented follow the DESPRO UP-10 template for local development projects and can be applied to small river restoration across Ukraine—especially for those most vulnerable to anthropogenic impacts. Granting nature conservation status to their coastal strips will help preserve valuable floodplain ecosystems. This study will be particularly useful for professionals in spatial planning and community management, as well as for researchers, educators, and students engaged in addressing the challenges of small river restoration.