Abstract. Estuaries are sources of nitrous oxide (N 2 O) and methane (CH 4 ) to the atmosphere. However, our present knowledge of N 2 O and CH 4 emissions from estuaries in the tropics is very limited because data are scarce. In this study, we present first measurements of dissolved N 2 O and CH 4 from two estuaries in a peat-dominated region of northwestern Borneo. Two campaigns (during the dry season in June 2013 and during the wet season in March 2014) were conducted in the estuaries of the Lupar and Saribas rivers. Median N 2 O concentrations ranged between 7.2 and 12.3 nmol L −1 and were higher in the marine end-member (13.0 ± 7.0 nmol L −1 ). CH 4 concentrations were low in the coastal ocean (3.6 ± 0.2 nmol L −1 ) and higher in the estuaries (medians between 10.6 and 64.0 nmol L −1 ). The respiration of abundant organic matter and presumably anthropogenic input caused slight eutrophication, which did not lead to hypoxia or enhanced N 2 O concentrations, however. Generally, N 2 O concentrations were not related to dissolved inorganic nitrogen concentrations. Thus, the use of an emission factor for the calculation of N 2 O emissions from the inorganic nitrogen load leads to an overestimation of the flux from the Lupar and Saribas estuaries. N 2 O was negatively correlated with salinity during the dry season, which suggests a riverine source. In contrast, N 2 O concentrations during the wet season were not correlated with salinity but locally enhanced within the estuaries, implying that there were additional estuarine sources during the wet (i.e., monsoon) season. Estuarine CH 4 distributions were not driven by freshwater input but rather by tidal variations. Both N 2 O and CH 4 concentrations were more variable during the wet season. We infer that the wet season dominates the variability of the N 2 O and CH 4 concentrations and subsequent emissions from tropical estuaries. Thus, we speculate that any changes in the Southeast Asian monsoon system will lead to changes in the N 2 O and CH 4 emissions from these systems. We also suggest that the ongoing cultivation of peat soil in Borneo is likely to increase N 2 O emissions from these estuaries, while the effect on CH 4 remains uncertain.