Carqueja (Baccharis crispa Spreng.) has been primarily used as a medicinal plant around the world. Commercially, the essential oil content of carqueja leaves is the most valuable crop productivity variable. We evaluated the effect of irrigation management in different growing seasons on the essential oil content of carqueja leaves using gas chromatography coupled with mass spectrometry. The experiment was conducted in a greenhouse located in Southern Brazil, where the crop was cultivated for two years in different growing seasons under six irrigation regimes: 25%, 50%, 75%, 100%, 125%, and 150% of the reference crop evapotranspiration (T25, T50, T75, T100, T125, and T150, respectively). A seasonal pattern was observed in the number of metabolites of sesquiterpenes and phenolics in the essential oil extracted from the biomass; this outcome was correlated with irrigation regimes and air temperature. Principal component and hierarchical cluster analyses were used to discriminate the influence of abiotic conditions on secondary metabolite profiles. Spathulenol was the most abundant compound in the essential oils (95.43%) collected during the summer (December–March) season during the third harvest (H3) at T150. The essential oil content was 8.84% ± 0.05% and 10.52% ± 0.10% in summer and winter (June–September), respectively, with T100 at 45 and 46 days after planting.