The Tubul-Raqui estuary is a coastal system off central Chile at 37°S, adjacent to an active coastal upwelling area, which undergoes rapid changes associated with natural and anthropogenic perturbations. Biogenic greenhouse gas cycling and the gas saturation levels are good indicators of microbial metabolism and trophic status in estuaries. The dissolved greenhouse gases CO2, CH4 and N2O and other biological and chemical variables were spatially recorded in this estuary over two seasons (summer and winter) and over one-half of one tidal cycle. Tidal and spatial variability of these gases indicated they had different origins within the system. Surface waters were always oversaturated in CO2 (up to 578%) and CH4 (up to 6200%) with respect to the atmosphere. But while CO2 seems to come from marine and in situ metabolism, CH4 appears to be more influenced by fluvial and adjacent salt marsh areas. In contrast, N2O was mostly undersaturated and sediments seem to be largely responsible for its consumption. Strong seasonal variability was also observed in CO2 and CH4 fluxes, being tenfold (from −319 to 714 mmol m−2 d-1) and fivefold (from 0.33 to 2.5 mmol m−2 d-1) higher, respectively, in the austral summer compared to winter. In contrast, only small seasonal differences in N2O fluxes were found ranging from −59 to 28 µmol m−2 d−1. These temporal patterns can be explained not only in terms of hydrological and nutrient balances within the system, but also by the influence of wind-driven upwelling processes. Additionally, potential effects of changes in nutrient load and freshwater discharge on net ecosystem metabolism (i.e., autotrophy or heterotrophy) and therefore, on the production/removal of greenhouse gases in this system were explored.