Coastal ecosystems host high levels of primary productivity leading to exceptionally dynamic elemental cycling in both water and sediments. In such environments, carbon is rapidly cycled leading to high rates of burial as organic matter and/or high rates of loss to the atmosphere and laterally to the coastal ocean in simpler forms, such as carbon dioxide (CO2) and methane (CH4). To better understand carbon cycling across these heterogeneous environments, new technologies beyond discrete sample collection and analysis are needed to characterize spatial and temporal variability. Here, we describe the ChemYak, an autonomous surface vehicle outfitted with a suite of in situ sensors, developed to achieve large spatial scale chemical mapping of these environments. Dissolved methane and carbon dioxide are measured by a laser spectrometer coupled to a gas extraction unit for continuous quantification during operation. The gas-powered vehicle is capable of rapidly surveying the coastal system with an endurance of up to 10 h at operating speeds in excess of 10 km h-1. Here, we demonstrate its ability to spatially characterize distributions of CO2, CH4, oxygen, and nitrate throughout a New England saltmarsh estuary.