Bioclogging in intermittent streams influences hyporheic flow, nutrient cycling, and ecosystem biodiversity. Disconnected pools, characterized by elevated nutrient concentrations and temperatures ranging from 20 to 45 degrees C, provide a unique setting for studying bioclogging dynamics in arid and semiarid regions. Despite this importance, the impact of temperature on microbial communities driving bioclogging remains underexplored. Through 77-day biofilm culture column experiments, hydrodynamic monitoring, sediment microbial community analysis, and resazurin tracer tests, this study investigates how different temperatures (20 degrees C, 30 degrees C, and 40 degrees C) shape microbial diversity, community interactions, and bioclogging processes. Results showed that microbial diversity increased with temperature, with the highest species richness and evenness observed at 40 degrees C. Proteobacteria, a dominant taxon, maintained broad ecological niches across all temperatures, whereas niche differentiation became more pronounced at 40 degrees C, reducing competition between taxa. Stochastic processes, such as random dispersal and migration, gained prominence, with migration rates (i.e., a dimensionless metric) rising from 0.47 at 20 degrees C to 0.86 at 40 degrees C. Bioclogging rates also declined as microbial activity concentrated near the sediment-water interface, resulting in a 21.4% reduction in clogging at 40 degrees C compared to 20 degrees C. These findings highlight the significant influence of temperature on microbial community assembly, sediment permeability, and bioclogging extent. They underscore the need to consider microbial dynamics in water resource management, particularly in arid regions where temperature-driven changes could affect nutrient cycling and water connectivity. Integrating microbial interactions and temperature effects into bioclogging models could enhance predictions of climate change impacts on stream ecosystems, providing a more comprehensive understanding of potential future scenarios.