Green roofs have been increasingly used to improve stormwater management, but poor vegetation performance on roof systems, varying with vegetation type, can degrade discharge quality. Biochar has been suggested as an effective substrate additive for green roofs to improve plant performance and discharge quality. However, research on the effects of biochar and vegetation on discharge quality in the long term is lacking and the underlying mechanisms involved are unclear. We examined the effects of biochar amendment and vegetation on discharge quality on organic-substrate green roofs with pre-grown sedum mats and direct-seeded native plants for three years and investigated the key factors influencing discharge quality. Sedum mats reduced the leaching of nutrients and particulate matter by 6–64% relative to native plants, largely due to the higher initial vegetation cover of the former. Biochar addition to sedum mat green roofs resulted in the best integrated water quality due to enhanced plant cover and sorption effects. Structural equation modeling revealed that nutrient leaching was primarily influenced by rainfall depth, time, vegetation cover, and substrate pH. Although biochar-amended sedum mats showed better discharge quality from organic-substrate green roofs, additional ecosystem services may be provided by native plants, suggesting future research to optimize plant composition and cover and biochar properties for sustainable green roofs.