In flowing waters, fluxes of greenhouse gases (GHGs), carbon dioxide (CO2) and methane (CH4), are products of dissolved gas concentrations and gas transfer velocity (k600). Although spatial patterns in lotic GHG concentrations and fluxes have been widely studied, temporal dynamics remain relatively understudied due to limited long-term, regularly collected concentration data. In addition, CO2 and CH4 have rarely been analyzed simultaneously. Here, we synthesized temporal concentration-k600-flux (C-k-F) patterns for CO2 and CH4 across 27 National Ecological Observatory Network (NEON) stream and river sites with monthly observations since 2016. We found that k600 was significantly negatively related to CO2 concentrations at 15 sites and to CH4 concentrations at 11 sites, suggesting inconsistent importance of k600 on the concentrations across sites. High fluxes were consistently associated with higher k600 for CO2 and higher concentrations for CH4. These results suggested that, temporally, CO2 flux was primarily controlled by physical gas exchange whereas CH4 flux was driven by supply across sites. This study provides the first synthesis of lotic GHG time-series data and offers a foundation for investigating site-specific and continental-scale temporal patterns and controls of lotic GHG concentrations and fluxes.