The Texas Commission on Environmental Quality (TCEQ) uses a Water Availability Modeling System (WAM) to support long-term regional and statewide water resources planning and management. The water availability studies are based on the modeling capabilities of the Water Rights Analysis Package (WRAP). This research improves the understanding of decision support tools for short-term river basin management. Current reservoir storage levels must be considered to assess short-term frequencies and reliabilities. Conditional reliability modeling (CRM) is used to assess the likelihood of meeting targets for instream flow, reservoir storage, water supply diversion and hydroelectric power generation in the near future (next month to next several years), conditioned upon preceding storage. This study uses data for the Brazos River Basin from the TCEQ WAM System to assess key complexities of water supply reliability analysis in general and conditional reliability modeling in particular. These complexities include uncertainties associated with river basin hydrology, estimating yield-reliability relationships for individual reservoirs and multiple reservoir systems, conventional long-term planning versus short-term adaptive management and other modeling and analysis issues. The modeling capabilities of WRAP were expanded to support near real-time operation of dams under various stream flow conditions. The sensitivity to changes in modeling options is assessed for short and long-term simulations. Traditional and newly developed methodologies for estimating firm yields and water supply reliabilities are evaluated. Guidelines are developed regarding the practical application of firm yield analyses and conditional reliability modeling. Important applications of this research include real-time decision support during drought and routinely recurring operational planning activities. A case study of the drought of 2009 uses the CRM features of WRAP for these applications.