The special session on “A global south perspective on tropical freshwater challenges” is an initiative of the Tropical Water Research Alliance (https://www.thetwra.org/en/), which aims to support collaboration among researchers in Australia and Brazil. Although tropical and subtropical rivers and wetlands harbour much of the world’s freshwater biodiversity, they are less well-studied than systems in temperate regions and are disproportionately affected by many contemporary anthropogenic threats, including hydropower development, land-based water pollution and water withdrawals. Given the ‘wicked’ nature of these environmental challenges, collaboration among the biophysical sciences is essential but often insufficient and a trans-disciplinary perspective is required that also considers the social, economic, and cultural dimensions of water management. Such expertise is seldom found in a single institution and research partnerships and networks are essential to enable such collaborations. Furthermore, the scientific community cannot address these challenges alone and the creation of links between public authorities, the private sector and civil society is needed to ensure that science can meet societal needs. In this session, we aim to highlight key management issues and knowledge gaps for tropical and subtropical freshwater systems across a range of countries and provide case studies of successful collaborations and partnerships. We hope that this will help to foster and support research collaborations across the global south.