In freshwater forested wetlands, bald cypress knees (Taxodium distichum (L.) Rich.) have the potential to emit large amounts of methane (CH₄), but only a few studies have examined their greenhouse gas contribution. In this study, we measured CH₄ fluxes associated with cypress knees across various climate and flooding gradients of the Mississippi River Alluvial Valley in southcentral United States. Greenhouse gases were measured using a portable gas analyzer with a custom-made chamber placed over the knees. We also conducted 3D lidar scans of knees using a smartphone to estimate the surface area and volume of knees. We investigated the following: (1) What parameters influence CH₄ fluxes (i.e., knee height, distance to stream, temperature, relative humidity, water level, precipitation)? and (2) Which type of knee shape measurement (i.e., cone, frustrum, or lidar scan) provides the best fit to model data while maximizing measurement efficiency? We found that knee CH₄ flux rates ranged from − 0.005 to 182 mmol m^− 2 d^− 1. There were positive correlations between CH₄ fluxes, water levels, and temperature, and a negative correlation with knee height. Sites that had been dry for longer periods of time emitted less CH₄ than sites where the soil remained saturated. The frustrum shape produced a knee volume estimate that was within 12% of lidar scans, whereas cone shapes underestimate knee dimensions (-100%). Further research of emissions and fluxes in cypress knees could fill knowledge gaps within the carbon cycle and could represent a major component of wetland CH₄ budgets.