Intermittent rivers comprise up to 60% of the total length of all river networks globally. Due to climate change impacts and water abstraction, stream intermittency is predicted to become more widespread in the future. Intermittent rivers may have “hot spots” or “hot moments” of biogeochemical activity due to rewetting of streambed sediments after drought likely creating unique structure-function patterns. This project’s goal was to mechanistically understand organic matter recalcitrance and bacterial/archaeal diversity differences in intermittent versus perennial stream reaches in a large urban watershed: San Antonio, Texas, USA. Seven intermittent and seven perennial stream reaches (referred to as “flow type”) were sampled for water chemistry, sediment respiration, sediment bacterial/archaeal communities (via 16S rRNA gene amplicon sequencing), and organic matter (OM) molecule characterization via Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) across baseflow (September 2023) and peak flow (February 2024). Preliminary results indicate dissolved total nitrogen (TN) did not vary across flow type but did vary across season: perennial sites had greater TN during the dry season whereas intermittent sites exhibited the opposite trend. Sediment respiration differed among flow types during the dry season only: intermittent sites with no water had ~71% lower respiration than intermittent sites flowing at time of sampling and perennial sites. Respiration did not differ across flow type during the wet season. Bacterial/archaeal diversity also differed between flow type: on average, intermittent sites had lower alpha diversity than in perennial sites. In sum, intermittent, urban rivers in this semi-arid climate experience long periods of no flow resulting in reduced aerobic respiration upon water return which is potentially, in part, due to lower survival of diverse microbial taxa in sediments. Further analysis includes OM characterization of specific structural categories present in sediments of sampling locations and deeper analysis of sediment microbiomes.