Environmental restoration in aquatic systems requires innovative approaches that combine scientific understanding, socioeconomic demands, and local stakeholder values into decisions. However, changing approaches to water management to address these requirements is difficult because of scientific and socioeconomic uncertainty and institutional barriers that can prevent implementation of alternative water management approaches. Current restoration efforts in the Atchafalaya River Basin (ARB) of Louisiana are faced with this challenge. Water management in the ARB has evolved from strong federal control to establish the ARB as a primary floodway of the Mississippi River and Tributaries Project to a state and federal collaboration to accommodate fish and wildlife resource promotion, recreational opportunities, and economic development. While management policy has expanded to include a growing number of stakeholders, the decision-making process has not kept pace. Current conflicts among many local stakeholder groups, due in part to their lack of involvement in the decision-making process, impede restoration efforts. The absence of a long-term collective vision for the ARB by both local stakeholder groups and numerous management agencies further confounds these efforts. Here, I propose a process to apply a structured decision making framework, a values-based approach that explicitly defines objectives, to promote stakeholder-driven restoration efforts in the ARB and to better prepare for and manage long-term environmental issues. The goals of this approach are: 1) to create a process founded on stakeholder values and supported by rigorous scientific assessment to meet management agency mandates and 2) to establish a structure for restoration planning in the ARB that incorporates current and future non-governmental stakeholders into a transparent decision-making process. Similar frameworks have been successful in other river basins and the structure of current restoration efforts in the ARB is well-suited to adopt a values-focused management framework. Next, I use flow-ecology relationships to evaluate ecosystem service trade-offs and complementarities in the ARB to assess the potential impacts of water management decisions. Flow-ecology relationships were used to explore complementary and trade-off relationships among 12 ecosystem services and related variables in the ARB. Results from Indicators of Hydrologic Alteration were reduced to four management-relevant hydrologic variables using principal components analysis. Multiple regression was used to determine flow-ecology relationships and Pearson correlation coefficients, along with regression results, were used to determine complementary and trade-off relationships among ecosystem services and related variables that were induced by flow. Seven ecosystem service variables had significant flow-ecology relationships for at least one hydrologic variable (R2 =0.19-0.64). River transportation and blue crab (Callinectes sapidus) landings exhibited a complementary relationship mediated by flow; whereas transportation and crawfish landings, crawfish landings and crappie (Pomoxis spp.) abundance, and blue crab landings and blue catfish (Ictalurus furcatus) abundance exhibited trade-off relationships. Other trade-off and complementary relationships among ecosystem services and related variables, however, were not related to flow. These results give insight into potential conflicts among stakeholders, can reduce the dimensions of management decisions, and provide initial hypotheses for experimental flow modifications. The final study in this dissertation proposes an environmental flow prescription for the highly altered ARB. The development of the ARB into a floodway has contributed to hydrologic changes basin-wide that have altered the river-floodplain interface threatening important ecosystems, notably the expansive baldcypress-water tupelo swamp forests. Analysis of the current flow regime reveals a 12-92% increase in mean monthly discharge over the past 80+ years, but a 24-43% decrease in mean monthly stage in large portions of the basin. Current restoration efforts only address the spatial distribution of water in local areas of the basin; however the timing, frequency, magnitude, and duration of ecologically important high and low flows are determined at the basin-wide scale by the daily implementation of a federal flow mandate that limits available water management options. We used current hydrologic conditions and established flow-ecology relationships from the literature to develop an environmental flow prescription for the ARB that provides basin-wide flow targets to complement ongoing restoration efforts. The result is an adaptive flow regime that strives to balance important flow-ecology relationships within a decision space limited by a federal flow mandate. We found that lengthening the implementation of the current flow mandate to monthly or quarterly time scales has high potential for success in meeting both the flow mandate and important flow-ecology relationships.