Both biotic and abiotic factors are involved in the seasonal variability of ecosystem respiration (R-e) and its aboveground (R-ag) and belowground (R-s) components. Knowledge of these factors is crutial to predict the respiration processes of structurally-distinct orchards under varying environmental conditions. This paper aims to characterize those factors in and across adult (AO) and young (YO) drip-irrigated citrus orchards over a 2-year period. Two methods for estimating R-e were used and compared. In the first one (C-method) R-e was calculated as the sum of R-ag and R-s components, with each being estimated using organ-specific and soil respiration models previously validated and calibrated from chamber-based respiration and biometric canopy measurements. The second method was based on the determination of nighttime R-e from data of early morning Net Ecosystem Exchange (NEE-method) provided by eddy covariance sensors located above the canopy. Estimates of R-e by the two methods compared reasonably well. The C-method indicated that Rs was the predominant component of R-e in both orchards, with a main peak in early spring (ratio R-s/R-e similar to 0.75 and 0.65 in AO and YO, respectively) during the period with no fruit load and minimum R-ag. Data obtained with the NEE-method were used to test the performance of functional relationships between R-e and abiotic factors (i.e., temperature through a Q(10) function, and soil water content). It was found that a model only based on abiotic factors was unable to explain the differences in R-e across sites; whereas accounting for canopy productivity and structure by introducing the leaf area index (LAI) as an additional driving variable notably increased the predictive power of the models in describing changes in R-e, both seasonally and across sites. The study suggested that biotic factors explained a large part of the differences in R-e between orchards, and that LAI could be an appropriate driving variable for predicting the impact of tree age and structural heterogeneity on R-e.