Vegetated surfaces in urban environments have the potential to improve building energy performance, reduce urban heat islands (UHI), and establish habitat connectivity between natural areas. However, most design and simulation tools lack integrated metrics to assess habitat fragmentation, suitable growing environments for plant species, or overall potential for biodiversity within urban environments. This research established a modeling framework that synthesizes data input on plant species, urban context, and climatic factors to forecast the habitat connectivity, select microclimatic conditions, and potential biodiversity benefits of integrating vegetated surfaces within urban environments. Utilizing ‘reconciliation ecology,’ the modeling framework combines design feedback on green roofs and walls to reduce habitat fragmentation, promote biodiversity, and create the potential for cities to support a range of threatened or endangered species.