This chapter delves into the multifaceted roles of aquatic parasites within natural ecosystems. It highlights both the negative and positive impacts these parasites can have on individual hosts, host populations, biodiversity and overall ecosystem health. The discussion covers how parasites influence various levels of biological organisation and ecosystem functions. It also explores how healthy ecosystems are defined and maintained, emphasising the roles of vigour, organisation and resilience. The complex interactions between parasites and their hosts are illustrated through numerous examples, spanning cases of behavioural modification, host–parasite coevolution, and broader ecological consequences stemming from those interactions. Understanding the interplay between parasites, hosts and ecosystems is presented as crucial for a comprehensive view of ecosystem dynamics.