Intermittent rivers and ephemeral streams (IRES) comprise over half of the global river network. Until recently, IRES have been under-studied, leading to a lack of protection despite their global prevalence and importance. In addition, research in IRES is a unique opportunity to examine how spatiotemporal variation in environmental drivers can impact assemblage-level responses. Although IRES research has expanded in recent years, 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 spatially explicit 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 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 community composition. Results indicate that AFDW in pools is lower in the intermittent middle reach than in the more perennial lower reach. Additionally, benthic AFDW differed by mesohabitat type, and was also affected by water temperature and canopy cover. Benthic chlorophyll-a concentrations do not differ between reaches or sampling occurrences; however, chlorophyll-a concentration was affected by water temperature and small-scale variation in velocity.