Symbioses are major drivers in ecology and evolution. Although nearly omnipresent in flowing waters, they remain poorly studied in these systems. To examine fundamental aspects of the ecology of symbioses in flowing-water systems, we use larval black flies as hosts and various fungi, nematodes, and protists as symbiotes, focusing on aspects of distribution, diversity, and scale. Most symbiotes of larval black flies are considered parasitic, although the dynamic nature of the relationship is becoming apparent for some systems in which it shifts along a continuum involving commensalism, mutualism, and parasitism. Perspective also is moving from a pairwise view of symbiotic associations to a multispecies network of interactions. Distributions of symbiotes are related to scale-dependent processes that influence the hosts and the stream habitats of the hosts; thus, characteristics of streams, as well as hosts, can be useful in predicting spatial patterns of symbiotes. As the taxonomy of symbiotes improves, so too does the understanding of ecological relationships of symbiosis, such as host specificity and patterns of diversity along spatial and temporal scales.