Ecosystem-based adaptation to climate change impacts, such as shoreline retreat, has been promoted at the international, national, and even local levels. However, among scientists, opinions about how to implement it in spatial-planning practices are varied. Science-based environmental factors, human wellbeing, and sustainable development can be strengthened by developing spatial-planning-based ecosystem adaptations (SPBEAs). Therefore, this article aims to assess how the SPBEA model can be developed within an area prone to shoreline retreat. A coastal area of the Sayung subdistrict in Central Java, Indonesia, was selected as a study area because it has experienced a massive shoreline retreat. A multicriteria analysis (MCA) method was employed for developing the model by using the geographic information system (GIS) technique of analysis, divided into three steps: the fishpond zone determination, which involved the analytical hierarchy process (AHP) method in the process of model development; the fishpond site determination; SPBEA fishpond site development. The results show that the SPBEA model is the best practice solution for combatting shoreline retreat because of tidal waves and/or sea-level rise. The spatial site management should empower the coastal protection zone and the sustainable fishpond zone by implementing a silvofishery approach.