Globally, freshwater ecosystems are under threat. The main threats come from catchment land-use changes, altered water regimes, eutrophication, invasive species, climate change and combinations of these factors. We need scientific research to respond to these challenges by providing solutions to halt the deterioration and improve the condition of our valuable freshwaters. This requires a good understanding of aquatic ecosystems, and the nature and scale of changes occurring. Macrophytes play a fundamental role in aquatic systems. They are good indicators of ecosystem health, as they are affected by run-off from agricultural, industrial or urban areas. On the other hand, alien macrophytes are increasingly invading aquatic systems all over the world. Improving our knowledge on the ecology and management of both native and alien plants is indispensable to address threats to freshwaters in order to protect and restore aquatic habitats. The International Aquatic Plants Group (IAPG) brings together scientists and practitioners based at universities, research and environmental organisations around the world. The main themes of the 15th symposium 2018 in New Zealand were biodiversity and conservation, management, invasive species, and ecosystem response and restoration. This Virtual Special Issue provides a comprehensive review from the symposium, addressing the ecology of native macrophytes, including those of conservation concern, and highly invasive alien macrophytes, and the implications of management interventions. In this editorial paper, we highlight insights and paradigms on the ecology and management of native and alien macrophytes gathered during the meeting.