Intermittent rivers and ephemeral streams (IRES) are relatively understudied, but important ecosystems in arid- and semi-arid regions. IRES are ecosystems where spatio-temporal variation in hydrologic regimes affect a diversity of ecosystem-level processes, such as nutrient cycling and ecosystem metabolism. Understanding how spatio-temporal variation in hydrological regimes affect nutrient concentrations and ecosystem metabolism is crucial for developing water resources management strategies. In this study, we examined the influence of seasonality and watershed positioning (i.e., upstream vs downstream), and hydrologic regime (perennial and temporally stable flows, intermittent flows, or seasonally variable but perennial flows) on rates of gross primary production (GPP), ecosystem respiration (ER), and terrestrial leaf litter decomposition rates the San Saba River (Texas, USA). We examined these processes at nine reaches that varied in hydrologic regime and watershed position across four seasonal periods (Fall, Winter, Spring, and Summer). We hypothesized that light and temperature would be principal drivers of GPP and ER, respectively, whereas hydrological characteristics, water temperature, and reach position in the drainage would more strongly influence nutrient dynamics and litter decomposition rates. Preliminary analysis indicates spatial variation in GPP, ER, and leaf litter input rates; we also found seasonal differences in ER and litter decomposition rates. Overall, the results of this study indicate that different facets of ecosystem functioning are affected by different environmental drivers working at different spatiotemporal scales. Additionally, findings from this study have critical implications for water resources management planning, especially under changing climates.