Intermittent rivers and ephemeral streams (IRES) comprise over half of the global river network. Research in IRES represents an opportunity to examine how spatiotemporal variation in environmental drivers can impact assemblage-level responses. Until recently, IRES have been under-studied, leading to a lack of protection despite their global prevalence and importance. Although IRES research has expanded, substantial questions remain about algal assemblages and their roles in community dynamics and ecosystem processes. Algae is the dominant primary producer in many IRES because of a lack of macrophytes and limited riparian vegetation in more arid regions. In this study, we collected benthic algae samples from riffles and pools at nine sites in the San Saba River (Texas, USA) throughout Summer 2024. The San Saba River has a hydrological gradient of flow intermittency and variability: the groundwater-fed upper reach has consistent perennial flow; the middle reach frequently undergoes drying and fragmentation; and the lower reach exhibits a more variable flow regime but typically maintains flow. We deployed unglazed ceramic tiles in riffle and pool mesohabitats at nine different study reaches and collected and redeployed tiles every three weeks. We additionally collected in situ limestone cobbles from mesohabitats at each site every three weeks. Algal biofilms were removed from tiles and rocks to estimate ash-free dry weight (AFDW), chlorophyll-a concentration, and algal assemblage composition. Results indicate that AFDW of cobbles was higher in pool mesohabitats and declined with increasing canopy cover. However, chlorophyll-a concentrations on tiles were higher in riffles than pools and declined with increasing canopy cover. Algal assemblage composition differed significantly between the different reaches of the river as well as the mesohabitats but did not vary significantly among sampling dates.