Helminth parasites of fish in marine systems are often considered to be generalists, lacking host specificity for both intermediate and definitive hosts. In addition, many parasites in marine waters possess life cycles consisting of long-lived larval stages residing in intermediate and paratenic hosts. These properties are believed to be adaptations to the long food chains and the low densities of organisms distributed over broad spatial scales that are characteristic of open marine systems. Moreover, such properties are predicted to lead to the homogenization of parasite communities among fish species. Yet, these communities can be relatively distinct among marine fishes. For benthos, the heterogeneous horizontal distribution of invertebrates and fish with respect to sediment quality and water depth contributes to the formation of distinct parasite communities. Similarly, for the pelagic realm, vertical partitioning of animals with depth will lead to the segregation of parasites among fish hosts. Within each habitat, resource partitioning in terms of dietary preferences of fish further contributes to the establishment of distinct parasite assemblages. Parasite distributions are predicted to be superimposed on distributional patterns of free-living animals that participate as hosts in parasite life cycles. The purpose of this review is first, to summarize distribution patterns of invertebrates and fish in the marine environment and relate these patterns to helminth transmission. Second, patterns of transmission in marine systems are interpreted in the context of food web structure. Consideration of the structure and dynamics of food webs permits predictions about the distribution and abundance of parasites. Lastly, parasites that influence food web structure by regulating the abundance of dominant host species are briefly considered in addition to the effects of pollution and exploitation on food webs and parasite transmission.