Increasingly water managers and scientists are working together to determine environmental flow recommendations for a variety of ecosystems. Successful recommendations require that water managers incorporate flexibility into their decision making process by adaptively managing water resources, and that scientists provide managers with best estimates of environmental flow needs, as there tend to be expectations for measurable “ecological returns.” Recent efforts by scientists and water managers to determine environmental flow recommendations highlight the need for improved methodologies. Environmental flow science and policy decisions currently fall into two categories: instream flows within rivers and freshwater inflows to bays and estuaries. While scientists and managers desire a better understanding of the impacts and processes operating within each category, little effort has been made to integrate the two. This workshop will focus on developing and improving suitable methodologies for guiding environmental flow recommendations within instream and coastal ecosystems. Workshop participants will review and critique existing methodologies. Discussions will identify categories of management objectives and the necessary environmental criteria for evaluating and developing suitable methodologies to achieve the stated objectives for these systems. Participants also will consider how to link the separate methodologies developed for instream flows and freshwater inflows to enhance environmental flow policy for the protection of aquatic ecosystems and the services they provide. Results of this workshop will be made available to the scientific community through publication, such as a report to Frontiers in Ecology and the Environment.