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Intermittent rivers and ephemeral streams (IRES) experience drying events, and they are becoming increasingly common due to climate change and anthropogenic water withdrawal. Despite their prevalence, IRES have been less studied than non-drying rivers, and more research is needed to understand their dynamics. This dissertation examines drying events' effects on the sediment microbial community structure and biogeochemistry in temperate IRES. First, a research study was carried out using an outdoor mesocosm setup to track changes in bacterial and fungal communities, microbial functions and properties of sediment-dissolved organic carbon during three different drying events. Results showed that drying duration and intensity and sediment organic matter content regulated river Spree sediment microbial community composition and biogeochemical processes during drying. The associated sediment respiration, assessed as CO2 flux, rapidly declined during all drying treatments, and Bacilli class became the most dominant bacteria after 90 days of drying, except in non-enriched sediment under the most intense drying. Second, a microcosm experiment was conducted to understand how sediment drying history and properties influence biogeochemical dynamics during an IRES expansion phase. Sediment respiration and nutrient release/retention rates were measured through flow resumption, and results showed that drying duration and intensity and sediment organic matter content regulated the dynamics of nutrients and respiration upon flow resumption. Under the most intense and prolonged drying, non-enriched sediment showed a lag response in respiration during the first day after flow resumption, while all other treatments had either a linear increase or a fast pulse in respiration. Finally, the long-term microbial succession in IRES sediment and soil in the experimental catchment of Chicken Creek was investigated. In 2008 and 2018, the sediment of three ephemeral streams and their adjacent soil was analyzed for the structure of the bacterial and fungal communities and microbial functions across different seasons. Results showed that environmental factors, such as vegetation type and organic matter content, mediated sediment and soil microbial succession in Chicken Creek. Ephemeral streams under spare and sporadic flow events remained unique ecosystems with distinctive microbial communities and biogeochemical dynamics, different from its riparian soil. Overall, this dissertation concludes that temperate IRES are dynamic ecosystems where dry-wet cycles and environmental factors modulate their sediment microbial community structure and function trajectories in the short- and long term.