The Amazon rainforest plays a critical role in the global carbon cycle, yet large uncertainties remain regarding its net carbon balance. Accurate estimates of net ecosystem exchange (NEE) require accounting for the CO₂ storage term, which is commonly derived from vertical CO₂ profile measurements that are scarcely available at long-term flux tower sites. Here, we evaluated three approaches for estimating canopy CO₂ storage at the Rebio Jaru forest site in Rondônia, Brazil: (1) a multi-point CO₂ profile (MPP), (2) a single-point profile (SPP) based on a closed-path gas analyzer, and (3) a single-point eddy covariance approach (SPE) using CO₂ measurements from an open-path gas analyzer. Although the methods operated simultaneously for less than two years, both simplified approaches showed strong agreement with the reference MPP method, with coefficients of determination of R² = 0.87 for SPP and R² = 0.79 for SPE, whereas neglecting the storage term resulted in poor agreement (R² = 0.24). Using the SPE approach, we reconstructed a 13-year NEE time series that revealed pronounced interannual variability, with the forest generally acting as a carbon sink during La Niña conditions and shifting toward a carbon source during El Niño events and during consecutive years due to drought legacy effects. The seasonal cycle exhibited a marked carbon source peak during the transition from the dry to the wet season, likely associated with enhanced litter decomposition and increased soil respiration following the first rainfall events after prolonged dry periods. These results demonstrate that simplified single-point approaches can reliably reconstruct long-term NEE dynamics and substantially improve estimates of Amazonian carbon balance at sites where complete CO₂ profile measurements are unavailable.