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The quality of water in many urban rivers in Latin America is increasingly degrading due to wastewater and runoff discharges from urban sprawl. Due to deficits in sanitary drainage systems, greywater is discharged to the stormwater drainage network generating a continuous dry-weather runoff that reaches rivers without treatment. One of the main challenges in the region is to achieve sustainable management of urban runoff for the recovery of rivers ecosystem integrity. However, retrofitting conventional centralized wastewater drainage networks into the existing urban grid represents important social, economic and technical challenges. This paper presents an alternative adaptive methodology for the design of Nature-based Solutions for decentralized urban runoff treatment. Through this study, technical solutions commonly used for stormwater management were adapted for dry-weather runoff treatment and co-designed for the particular conditions of a representative study area, considering space availability as the main constraining factor for retrofitting in urban areas. The application of a co-design process in a dense neighbourhood of the Great Metropolitan area of Costa Rica brought to light valuable insights about conditions that could be hindering the implementation of NBS infrastructures in Latin America.