The possible impact of El Niño–Southern Oscillation (ENSO) events on the main components of CO2 and H2O fluxes in a pristine mountainous tropical rainforest growing in Central Sulawesi in Indonesia is described. The fluxes were continuously measured using the eddy covariance method for the period from January 2004 to June 2008. During this period, two episodes of El Niño and one episode of La Niña were observed. All these ENSO episodes had moderate intensity and were of Central Pacific type. The temporal variability analysis of the main meteorological parameters and components of CO2 and H2O exchange showed a very high sensitivity of Evapotranspiration (ET) and Gross Primary Production (GPP) of the tropical rain forest to meteorological variations caused by both El Niño and La Niña episodes. Incoming solar radiation is the main governing factor that is responsible for ET and GPP variability. Ecosystem Respiration (RE) dynamics depend mainly on the air temperature changes and are almost insensitive to ENSO. Changes of precipitation due to moderate ENSO events did not cause any notable effect on ET and GPP, mainly because of sufficient soil moisture conditions even in periods of anomalous reduction of precipitation in the region.