Green roofs are increasingly being implemented in cities for their multiple environmental benefits. Their optimal design requires an appropriate selection of components, including substrates and plant species, to ensure local sustainability in the long term. The present study seeks to assess the runoff quality and quantity of extensive green roofs located in Bogotá (Colombia). The assessment consists of testing different substrates, designed using locally available constituents and a selection of native species. The best performing substrate mixtures, in terms of runoff volume reduction and plant establishment, were jointly evaluated with three native species (i.e., Paepalanthus alpinus, Achryrocline bogotensis and Echeveria ballsii). On average, engineered substrates presented significantly lower concentrations in several water quality parameters (electric conductivity, total phosphorus, phosphates, Total Kjeldahl Nitrogen, nitrates, nitrites, color, biological oxygen demand and chemical oxygen demand) than the commercial extensive substrate used as control. The species Paepalanthus alpinus and Echeveria ballsii showed significant establishment and were considered potentially suitable species for green roofs in Bogotá. The obtained results, therefore, provide recommendations for green roof design in neotropical mountain climate conditions.