Conserving river biota will require innovative approaches that foster and utilize scientific understanding of ecosystem responses to alternative river-management scenarios. We describe ecological and societal issues involved in flow management of a section of the Tallapoosa River (Alabama, U.S.A.) in which a species-rich native fauna is adversely affected by flow alteration by an upstream hydropower dam. We hypothesize that depleted Iow flows, flow instability and thermal alteration resulting from pulsed flow releases at the hydropower dam are most responsible for changes in the Tallapoosa River biota. However, existing data are insufficient to prescribe with certainty minimum flow levels or the frequency and duration of stable flow periods that would be necessary or sufficient to protect riverine biotic integrity. Rather than negotiate a specific change in the flow regime, we propose that stakeholders--including management agencies, the power utility, and river advocates--engage in a process of adaptive-flow management. This process would require that stakeholders (1) develop and agree to management objectives; (2) model hypothesized relations between dam operations and management objectives; (3) implement a change in dam operations; and (4) evaluate biological responses and other stakeholder benefits through an externally reviewed monitoring program. Models would be updated with monitoring data and stakeholders would agree to further modify flow regimes as necessary to achieve management objectives. A primary obstacle to adaptive management will be a perceived uncertainty of future costs for the power utility and other stakeholders. However, an adaptive, iterative approach offers the best opportunity for improving flow regimes for native biota while gaining information critical to guiding management decisions in other flow-regulated rivers.