Peatlands are globally significant stores of soil carbon, where local methane (CH4) emissions are strongly linked to water table position and microtopography. Historically, these factors have been difficult to measure in the field, constraining our capacity to observe local patterns of variability. In this paper, we show how remote sensing surveys conducted from unmanned aerial vehicle (UAV) platforms can be used to map microtopography and depth to water over large areas with good accuracy, paving the way for spatially explicit estimates of CH4 emissions. This approach enabled us to observe—for the first time—the effects of low‐impact seismic lines (LIS; petroleum exploration corridors) on surface morphology and CH4 emissions in a treed‐bog ecosystem in northern Alberta, Canada. Through compaction, LIS lines were found to flatten the observed range in microtopographic elevation by 46 cm and decrease mean depth to water by 15.4 cm, compared to surrounding undisturbed conditions. These alterations are projected to increase CH4 emissions by 20–120% relative to undisturbed areas in our study area, which translates to a total rise of 0.011–0.027 kg CH4 day−1 per linear kilometer of LIS (~2 m wide). The ~16 km of LIS present at our 61 ha study site were predicted to boost CH4 emissions by 20–70 kg between May and September 2016.