The variability and drivers of carbon and water fluxes and their relationship to ecosystem water use efficiency (WUE) in natural ecosystems of southern South America are still poorly understood. For 8 years (2015-2022), we measured carbon dioxide net ecosystem exchange (NEE) and evapotranspiration (ET) using eddy covariance towers in a temperate rainforest and a peatland in southern Chile. NEE was partitioned into gross primary productivity (GPP) and ecosystem respiration ( R eco ), while ET was partitioned into evaporation ( E ) and transpiration ( T ) and used to estimate different expressions of ecosystem WUE. We then used the correlation between detrended time series and structural equation modelling to identify the main environmental drivers of WUE, GPP, ET, E and T . The results showed that the forest was a consistent carbon sink ( - 486 +/- 23 g C m - 2 yr - 1 ), while the peatland was, on average, a small source (33 +/- 21 g C m - 2 yr - 1 ). WUE is low in both ecosystems and likely explained by the high annual precipitation in this region ( similar to 2100 mm). Only expressions of WUE that included atmospheric water demand showed seasonal variation. Variations in WUE were related more to changes in ET than to changes in GPP, while T remained relatively stable, accounting for around 47 % of ET for most of the study period. For both ecosystems, E increased with higher global radiation and higher surface conductance and when the water table was closer to the surface. Higher values for E were also found with increased wind speeds in the forest and higher air temperatures in the peatland. The absence of a close relationship between ET and GPP is likely related to the dominance of plant species that either do not have stomata (i.e. mosses in the peatland or epiphytes in the forest) or have poor stomatal control (i.e. anisohydric tree species in the forest). The observed increase in potential ET in the last 2 decades and the projected drought in this region suggests that WUE could increase in these ecosystems, particularly in the forest, where stomatal control may be more significant.