Freshwater fish populations are under threat in a rapidly changing environment. Many of these impacts on individual fish health will be indirect and mediated by the microbial landscape. Upon hatching, fish start off with a naïve gut —a blank slate which quickly becomes colonized by microbes present in the environment. The community of microbes that establish is a result of a mix of deterministic processes such as host genetic and immune factors, diet, and physiology and stochastic processes like priority effects, ecological drift, and dispersal limitations of the microbes. To better understand the connection between the microbial landscape and fish health, we used 16S metabarcoding to describe the gut microbiomes of 3 fish species in the Colorado River (Rainbow Trout, Humpback Chub, and Flannelmouth Sucker). A total of 250 fish fecal samples were collected across 24 sites in the Colorado River, Grand Canyon. After strictly filtering the sequencing data to only analyze sequence variants with a relative abundance greater than 0.05% of a sample, we found an average of 179 sequence variants representing seven major phyla across fish fecal samples. However, the total diversity across samples was 2,229 sequence variants. The discrepancy is driven by high turnover in community composition. Distance based redundancy analysis showed spatial distance constrained a greater proportion of the variance in community composition than host related variables such as fish species, size class, or condition factor, or a suite of environmental variables related to water chemistry. These results indicate that stochastic processes dominate the community composition of fish gut microbiomes in the Colorado River, and further analyses are needed to link differences in fish gut microbiomes to changing environmental factors.