To determine types of fungi in the water and associated with the benthic amphipod Diporeia spp., samples were collected at various depths in Lake Michigan in an area where the Diporeia population was in a severe state of decline. No fungi were found associated with living, freshly-dead, or dried Diporeia cultured separately from Lake Michigan water. When dead Diporeia and other organic substrates (snake skin and hemp seeds) were used to grow fungi in Lake Michigan water, a rich and diverse fungal and water mold community was revealed. A total of 31 species were found, with the most common genera being Achlya, Aphanomyces, Myzocytium, and Pythium. In general, species were homogeneously distributed in the water; that is, few differences were found in species richness between nearshore (10–15 m) and offshore (60–80 m) waters, and between near-surface (1 m) and near-bottom waters (1 m off bottom). Sampling occurred during the unstratified period (April and October) to maximize the number of species collected, which may have contributed to the uniform spatial pattern observed. While conclusions must be placed in context with our methods of detection, we found no evidence that a fungal infestation was associated with Diporeia in this region of the lake.