There is a broad consensus that riparian buffers provide environmental benefits and increase resilience to climate change. In this study, we examined the potential benefits of multi-zone riparian buffers with outer layers planted in perennial crops (i.e., partially harvested buffers). This was accomplished by developing a simplified regional modeling tool, BioVEST, which was applied in the Mid-Atlantic region of the USA. Our analysis revealed that a substantial portion of variable costs to produce biomass for energy can potentially be offset by values provided by ecosystem services from partially harvested riparian buffers. Ecosystem services were monetized and found to represent a substantial fraction (median = ~42%) of variable crop production cost. Simulated water-quality improvements and carbon benefits generally occurred where buffer area was available, but hotspots occurred in different watersheds, suggesting potential trade-offs in decisions about buffer locations. A portion of buffers could be eligible for ecosystem service payments under US government incentive programs. Partially harvested buffers could represent a sustainable and climate-resilient part of multi-functional agricultural landscapes, and one that could become economically viable if farmers are able to reap the value of providing ecosystem services and if logistical challenges are resolved. Our results suggest that payments for ecosystem services can close the gap between what biorefineries are willing to pay and what landowners are willing to accept to grow and harvest perennials along streams.