In this study, we developed a methodology for evaluating holistic sustainability of alternative riparian buffer zone (RBZ) designs or decision management objectives. We demonstrated the methodology separately in three 12-digit Hydrologic Unit Code watersheds in the southeastern USA. We adapted the RBZ - hydrologic and water quality system assessment data of dissolved oxygen, total phosphorus, total nitrogen, total suspended solids - sediment, and biochemical oxygen demand, recently published by U.S. EPA, as environmental indicators. We calculated 20-year net present value costs as economic indicators using the costs data published by the Natural Resources Conservation Service. The holistic sustainability assessments using data envelopment analysis revealed urban RBZ to be the most sustainable (with holistic sustainability score of 1.00) across all watersheds. This dataset is associated with the following publication: Ghimire, S., A. Nayak, J. Corona, R. Parmar, R. Srinivasan, K. Mendoza, and J. Johnston. Holistic Sustainability Assessment of Riparian Buffer Designs: Evaluation of Alternative Buffer Policy Scenarios Integrating Stream Water Quality and Costs. Sustainability. MDPI, Basel, SWITZERLAND, 14(19): 12278, (2022).