Three deepwater hydrocarbon seep sites in the northern Gulf of Mexico that feature near-seafloor gas hydrates, MC118 (depth = 900 m), GC600 (depth = 1250 m) and GC185 (depth = 550 m), were investigated during the Remote Sensing and Sea-Truth Measurements of Methane Flux to the Atmosphere (HYFLUX) study in July 2009. Continuous measurements of air and sea surface concentrations of methane were made to obtain high spatial and temporal resolution of the diffusive net sea-to-air fluxes. The atmospheric methane fluctuated between 1.70 and 2.40 parts per million (ppm) during the entire cruise except for high concentrations (up to 4.01 ppm) sampled during the end of the occupation of GC600 and the transit between GC600 and GC185. In conjunction with air-mass back trajectory analysis, these high concentrations are likely from a localized methane source to the atmosphere. Methane concentrations in surface seawater and methane net sea-to-air fluxes show high temporal and spatial variability within and between sites. The presence of ethane and propane in the surface seawater indicates a thermogenic source in the plume areas, suggesting the surface methane could be at least partly attributable to transport from the deepwater hydrocarbon seeps. Results from interpolations within the survey areas show the daily methane fluxes to the atmosphere at the three sites range from 0.744 to 300 mol d−1. Extrapolating the highest daily sea-to-air flux of methane to other deepwater seeps in the northern Gulf of Mexico suggests that the net diffusive sea-to-air flux from deepwater hydrocarbon seeps in this region is an insignificant source to the atmospheric methane.