Freshwater biodiversity is under constant threat from a range of anthropogenic stressors. Using South Africa's Phongolo River and floodplain (PRF) as a study case, the aim of this chapter is to provide an overview of the conservation and management of freshwater biodiversity in a highly diverse subtropical ecosystem. The PRF is the largest floodplain system in South Africa which is severely threatened by irregularly controlled flood releases from a large upstream dam, prolonged drought, deteriorating water quality, organic pollutants and the increasing dependence of the local communities. Based on a decade of survey of the PRF conducted from 2010 to 2020, this chapter highlights the current diversity of aquatic organisms (invertebrates, fishes, frogs and their parasitic fauna), followed by an overview of their biological and physical stressors. The current challenges in the management of the aquatic biodiversity of this region and a way forward to conservation strategies are also addressed in this chapter.