<p><strong>Abstract.</strong> Dissolved inorganic nitrogen (DIN), including nitrate, nitrite and ammonium, frequently acts as the limitation for primary productivity. Our study focused on the transport and transformation of dissolved inorganic nitrogen in a tropical estuary, i.e. Rajang river estuary, in Borneo, Malaysia. Three cruises were conducted in August 2016, February&#8211;March and September 2017, covering both dry and wet seasons. Before entering the coastal delta, decomposition of the terrestrial organic matter and the subsequent soil leaching was assumed to be the main source of DIN in the river water. In the estuary, decomposition of dissolved organic nitrogen was an additional DIN source, which markedly increased DIN concentrations in August 2016 (dry season). In the wet season (February 2017), ammonium concentration showed a relatively conservative distribution during the mixing and nitrate addition was weak. In September 2017 (dry season), La Ni&#241;a induced high precipitation and discharge rates, decreased reaction intensities of ammonification and nitrification and hence the distribution of DIN species in the estuary water was similar with the trend found in the wet season. The magnitude of riverine DIN flux varied between 77.2 and 101.5&#8201;ton&#8201;N&#8201;d<sup>-1</sup>, which might be an important support for the coastal primary productivity.</p>