Changes related to climate and increased groundwater extraction can cause rivers that were once perennial to experience intermittent flows. These altered drying and wetting patterns can shape the composition and abundance of primary producers, like algae, over time and space to alter food webs and river nutrient dynamics. Some diatoms, and cyanobacteria, especially those that form mats or produce mucilage, can tolerate or even thrive in conditions of low or intermittent flow and warm temperatures. However, they are generally less palatable to grazers, and cyanobacteria can have lower nutritional quality and produce toxins. Thus, shifts in what taxa dominate or produce more biomass can have cascading effects throughout the river ecosystem. To investigate changes in periphyton assemblages within the San Saba and Concho Rivers in Texas, we collected samples from epilithic composites scraped from three riffle cobbles at each site during contrasting flow regimes: a low-flow year (2021) and a high-flow year (2023). We determined the relative abundance of cyanobacteria and other algal groups (reds, greens, diatoms) using microscopic counts and fluid imaging (FlowCam5000®). Assemblages were further categorized into functional groups and compared across flow conditions. Early explorations of the data suggest that sediment composition in part shaped differences between assemblages dominated by cyanobacteria or diatoms. Filamentous, mat-forming cyanobacteria commonly occurred. Changes in temperature and water quality also influenced the abundance of more sensitive groups like red alga. While the FlowCam can provide valuable insight into larger periphyton groups and functional categories, a more detailed analysis at the species level, particularly for diatoms, may provide more nuanced information on the response to the complex river conditions created with flow intermittency. The role of primary producers over time and space in intermittent rivers needs further research, especially where the rate of change or degree of variability in flow dynamics is less predictable.