Within the earth's atmosphere, methane (CH 4 ) is one of the most important absorbers of infrared energy. It is recognized that coastal areas contribute higher amounts of CH 4 emission; however, there is a lack of accurate estimates for these areas. This is particularly evident within the extensive northern fjord region of Chilean Patagonia, which has one of the highest freshwater runoffs in the world. Oceanographic and biogeochemical variables were analyzed between the Reloncaví fjord (41°S) and the Interior Sea of Chiloé (ISC) (43°S), during the 2013 austral winter. Freshwater runoff into the fjord influences salinity distribution, which clearly delimits the surface (<5 m depth) and subsurface layers (>5 m depth), and also separates the estuarine area from the marine area. In the estuary, the highest CH 4 levels are generally observed in the cold and brackish nutrient-depleted surface waters (N-and P-depleted), ranging from 16.97 to 151.4 nM (mean ± SD 52.20 ± 46.49), equivalent to 640-4537% saturation except for the case of Si(OH) 4 . Conversely, subsurface waters have lower CH 4 levels, fluctuating from 14.3 to 29.6 nM (mean ± SD 22.75 ± 4.36 nM) or 552-1087% saturation. A significant negative correlation was observed between salinity and CH 4 , and a positive correlation between Si(OH) 4 and CH 4 , suggesting that some of the CH 4 in estuarine water is due to continental runoff. Furthermore, the accumulation of seston and/or plankton at the pycnocline may potentially generate the accumulation of CH 4 via microbial processes, as observed in estuarine waters. By contrast, the marine area (the ISC), which is predominantly made up of modified subantarctic water, has a relatively homogenous CH 4 distribution (mean ± SD 9.84 ± 6.20 nM). In comparison with other estuaries, the Reloncaví fjord is a moderate source of CH 4 to the atmosphere, with effluxes ranging from 23.9 to 136 μmol m. This is almost double the levels obs e r v e d i n t h e I S C , w h i c h r a n g e s f r o m 2 2 . 2 t o 46.6 μmol m −2 day −1. Considering that Chilean Patagonia has numerous other fjord systems that are geomorphologically alike, and in some cases have much greater freshwater discharge, this study highlights their potential to be a significant natural source of this greenhouse gas.