Riparian ecosystems are a critical element of the landscape, especially in agricultural and other human-dominated landscapes (Capon et al. 2013; Capon and Pettit 2018). We define riparian ecosystems broadly here as those areas spatially (and temporally) adjacent to watercourses and waterbodies that influence these aquatic ecosystems and which, in turn, are influenced by them, largely through hydrological connectivity. Defined in this way, riparian ecosystems therefore include floodplains as well as channels and wetlands during dry phases. Such ecosystems are disproportionately valuable with respect to the area they occupy due to their key role in many essential ecological functions and in supporting much biodiversity (Capon et al. 2013). Riparian ecosystems are also crucial to the provision of many ecosystem services benefitting people. Furthermore, there is increasing recognition that these values are likely to grow under a changing climate and with increasing human pressures on natural ecosystems in the Anthropocene (Capon et al. 2013). Understanding the ecosystem services provided by riparian ecosystems, and the factors driving these, is therefore vital for effective natural resources management in agro-ecological landscapes. Cotton farms occupy significant areas of Australia’s inland catchments, especially in the northern Murray-Darling Basin straddling the Queensland and New South Wales borders. These farms typically comprise large areas of relatively natural ecosystems in addition to their productive and more intensely managed areas. In lowland regions, most of these natural ecosystems are likely to be riparian, including floodplain, ecosystems. Consequently, there is a need to understand the values, threats and management associated with riparian ecosystems in these landscapes to support effective management of these unique landscapes and their biodiversity and to promote sustainable cotton farming into the future. This report provides an overview of work conducted by Griffith University on behalf of the Cotton Research and Development Corporation between 2016 and 2019 to address knowledge gaps associated with the management of natural ecosystems on Australian cotton farms for the provision of ecosystem services.