AbstractNearshore environments are typically supersaturated with the potent greenhouse gases methane and carbon dioxide, due to intense remineralization of the elevated supply of organic carbon in these systems. These environments are characterized by overlapping biogeochemical gradients and heterogeneous morphology, and the overall spatial variability in nearshore greenhouse gas concentrations remains unclear. We measured surface water partial pressures of carbon dioxide and methane synoptically with water quality parameters in the coastal Baltic Sea, covering two ice‐free seasons. The high‐frequency flow‐through data revealed sites with recurring very high partial pressures of carbon dioxide and methane (i.e., hot spots) scattered around the 50 km × 40 km study area, exceeding overall partial pressure averages by 455 μatm (CH4) and 2396 μatm (CO2). High partial pressures were linked with elevated inputs of allochthonous and autochthonous organic matter, underpinning the major role of organic enrichment of coastal environments in global carbon cycling.