The Mekong River basin in Southeast Asia is one of the world's most productive and diverse ecosystems. Originating from the Tibetan Plateau, for much of its history the river flowed freely, draining parts of China, Myanmar, Thailand, Lao PDR, Cambodia and Vietnam on its way to the South China Sea. Currently, dams are being constructed at a rapid pace in China on the upper portion of the river, and on the river's tributaries throughout the basin, with plans to build dams on the lower mainstream Mekong River as well. These dams could trap a significant fraction of the 160 million metric tons of sediment annually transported by the river, thereby preventing the sediment from maintaining the basin's geomorphologic features, and from transporting the nutrients that support ecosystem productivity. This dissertation describes the development of a methodology to (1) identify reservoirs that could significantly alter the natural sediment regime, (2) assess alternative dam siting, design and operating policies that could improve sediment passage compared to current plans, and (3) quantify the losses in hydropower production that may be necessary to achieve improved sediment passage. To permit such evaluations, a sediment simulation model, SedSim, was developed in partnership with various water resources and energy ministries in Cambodia, Lao PDR and Vietnam. The model implements a daily time-step mass-balance simulation of flow and sediment to predict the spatial and temporal accumulation, depletion, and distribution of sediment in river reaches and in reservoirs under different flow and sediment management policies. This methodology is applied to dams on the transboundary Sre Pok, Se San and Se Kong tributaries of the Mekong, as well as on the mainstream Mekong River. Results from applying this methodology suggest that various changes to the siting, design and operating policies of reservoirs can significantly improve sediment passage through and around reservoirs, but that in many cases, significant sacrifices in energy production will be required to achieve the improved sediment passage.