<p><strong>Abstract.</strong> Nitrous oxide (N<sub>2</sub>O) and methane (CH<sub>4</sub>) are atmospheric trace gases which play important roles of the climate and atmospheric chemistry of the Earth. However, little is known about their emissions from rivers and estuaries which seem to contribute significantly to the atmospheric budget of both gases. To this end concentrations of N<sub>2</sub>O and CH<sub>4</sub> were measured in the Rajang, Maludam, Sebuyau and Simunjan Rivers draining peatland in northwestern (NW) Borneo during two campaigns in March and September 2017. The Rajang River was additionally sampled in August 2016 and the Samusam and Sematan Rivers were additionally sampled in March 2017. The Maludam, Sebuyau, and Simunjan Rivers are typical "blackwater" rivers with very low pH, very high dissolved organic carbon (DOC) concentrations and very low O<sub>2</sub> concentrations. The spatial and temporal variability of N<sub>2</sub>O and CH<sub>4</sub> concentrations (saturations) in the six rivers/estuaries was large and ranged from 2.0&#8201;nmol&#8201;L<sup>&#8722;1</sup> (28&#8201;%) to 41.4&#8201;nmol&#8201;L<sup>&#8722;1</sup> (570&#8201;%) and from 2.5&#8201;nmol&#8201;L<sup>&#8722;1</sup> (106&#8201;%) to 1372&#8201;nmol&#8201;L<sup>&#8722;1</sup> (57,459&#8201;%), respectively. We found no overall trends of N<sub>2</sub>O with O<sub>2</sub> or NO<sub>3</sub><sup>&#8722;</sup>, NO<sub>2</sub><sup>&#8722;</sup>, NH<sub>4</sub><sup>+</sup> and there were no trends of CH<sub>4</sub> with O<sub>2</sub> or dissolved nutrients or DOC. N<sub>2</sub>O concentrations showed a positive linear correlation with rainfall. We conclude, therefore, that rainfall is the main factor determining the riverine N<sub>2</sub>O concentrations since N<sub>2</sub>O production/consumption in the "blackwater" rivers themselves seems to be unlikely because of the low pH. In contrast CH<sub>4</sub> concentrations showed an inverse relationship with rainfall. CH<sub>4</sub> concentrations were highest at salinity&#8201;=&#8201;0 and most probably result from methanogenesis as part of the decomposition of organic matter under anoxic conditions. We speculate that CH<sub>4</sub> oxidation, which can be high when the water discharge is high (e.g. after rainfall events), is responsible for the decrease of the CH<sub>4</sub> concentrations along the salinity gradients. The rivers and estuaries studied here were an overall net source of N<sub>2</sub>O and CH<sub>4</sub> to the atmosphere. The total annual N<sub>2</sub>O and CH<sub>4</sub> emissions were 1.09&#8201;Gg&#8201;N<sub>2</sub>O&#8201;yr-1 (0.7&#8201;Gg&#8201;N&#8201;yr-1) and 23.8&#8201;Gg&#8201;CH<sub>4</sub>&#8201;yr-1, respectively. This represents about 0.3&#8211;0.7&#8201;% of the global annual riverine and estuarine N<sub>2</sub>O emissions and about 0.1&#8211;1&#8201;% of the global riverine and estuarine CH<sub>4</sub> emissions. Therefore, we conclude that rivers and estuaries in NW Borneo &#8211;despite the fact their water area covers only 0.05&#8201;% of the global river/estuarine area&#8211; contribute significantly to global riverine and estuarine emissions of N<sub>2</sub>O and CH<sub>4</sub>.</p>