Yi’an Reservoir is located on a major tributary of the Baoquan River and hosts abundant aquatic resources, with Cyprinus carpio, Carassius auratus, and Hemiculter leucisculus as the dominant fish species. Water quality parameters significantly shape fish gut microbiota, which in turn plays a crucial role in host physiological functions. This study aimed to characterize the water quality parameters in Yi’an Reservoir and identify the microbial communities in both the aquatic environment and fish guts (C. carpio, C. auratus, and H. leucisculus) through 16S ribosomal RNA sequencing. The objective was to examine the associations of water quality parameters and aquatic environmental microbiota with the assembly of gut microbial communities in fish inhabiting this reservoir system. The water quality parameters showed significant site-specific differences, of which temperature and dissolved oxygen were highest at Location B, while pH was highest at Location A. The Cyanobium_PCC-6307 was identified as a major differentially abundant taxon at the genera level across different sampling sites. Furthermore, the gut microbiota of the same fish species exhibited substantial variation across different sampling sites. Redundancy analysis identified distinct environmental drivers at each location. Specifically, pH, conductivity, and total dissolved solids (TDS) showed positive correlations with the gut microbiota at Location A. In contrast, temperature, dissolved oxygen (DO), and the environmental abundance of Cyanobium PCC-6307 were positively correlated with the gut microbiota at Locations B and C. This study provides important insights for the conservation and management of aquatic resources in reservoir ecosystems.