Parasitism is increasingly recognised as a significant determinant of composition and structure of natural communities across ecosystems. In this chapter, a large amount of evidence from the aquatic realm is brought together to highlight the multitude of processes through which parasites impact aquatic community structure. There are three main ways by which parasites affecting community structure are emphasised: (1) direct effects through differential regulation of host populations; (2) density-mediated indirect effects through modification of biotic processes such as predation, herbivory, facilitation and inhibition; and (3) trait-mediated indirect effects through altered phenotype of infected host species that often act as keystone species or ecosystem engineers in the community. Selected studies are treated in-depth to illustrate the ways parasites modify aquatic communities, involving a variety of host organisms such as monocotyledons, gastropods, bivalves, amphipods, echinoderms and fishes, as well as parasites ranging from protists to trematodes and nematodes, among others. This synthesis concludes by stressing that the available evidence does not equivocally support the contemporary theory that parasitism generally acts to maintain biodiversity. Rather, the qualitative effect is context-dependent, determined by the ecological roles of involved host species.