More than half of the river miles in the United States are characterized by intermittent flow conditions, and this proportion is expected to increase as a result of climate change and anthropogenic activities (e.g., groundwater pumping). Despite the ubiquity of non-perennial streams, the effect of stream drying on ecosystem function is not well understood. Our goal is to understand how the frequency and duration of stream drying affects ecosystem metabolism. Ecosystem metabolism, which represents the dual processes of gross primary production (GPP) and ecosystem respiration (ER), is a key metric of stream ecosystem function that integrates nutrient and carbon cycling. Using USGS, NEON, and field-collected data, we estimated monthly ecosystem metabolism from 37 USGS gages, 2 NEON sites, and 6 additional sites classified as non-perennial. Linear mixed models revealed that temperature and precipitation were the dominant controls on both GPP and ER, while drying metrics showed more nuanced effects. Specifically, the duration of flow decline before stream drying negatively influenced GPP. Low-flow event frequency positively influenced ER, consistent with microbial respiration pulses following rewetting events. Notably, the duration of individual drying events showed minimal effects on either metabolic process, suggesting that drying time may be more important than absolute dry period length. These findings indicate that increasing frequency of drying under future climate scenarios may alter stream carbon cycling through repeated drying-rewetting cycles rather than through extended drought duration alone.