Wetlands and their ability to mitigate climate change motivates restorative and protective action; however, scientific understanding of land-atmosphere interactions is restricted by our limited continuous observations of gaseous fluxes. Many wetlands are small in spatial scale and embedded in forested landscapes. Yet, little is known about how the relative sheltering of forests affects net carbon (C) and energy balance. Here, we analyze coterminous USGS and Ameriflux eddy covariance flux tower observations over 3 years in two shrub fens in Northern Wisconsin, one more sheltered (US-ALQ) than the other (US-Los). Unsurprisingly, the open site showed higher overall wind speeds. This should have implications for atmospheric fluxes in wetlands as wind-forced processes are essential in promoting gas exchange over water. While both sites had similar half-hourly net ecosystem exchange of CO2 (NEE) during daytime, there were significant differences in nighttime NEE, as well as in net radiation partitioning in early spring and late summer. Sensible heat (H) fluxes were smaller at the sheltered fen except for the months of July–September. In contrast, latent heat (LE) fluxes were higher in every month except July. Additionally, sheltered fen ecosystem respiration had a weaker linear correlation with air temperature (R: 0.08 vs. 0.57 for the open fen). Our work suggests that canopy sheltering does not cause significant differences in half-hourly NEE during the day, but rather the largest differences such as lower CO2 emissions occur at nighttime due to higher variance at very low wind speeds. Sheltering also influenced direction of air flow, mean wind speeds in day vs. night, energy balance, and sensible and latent heat fluxes. We discuss implications of these findings for wetland restoration.