Many ecophysiological and biogeochemical processes respond rapidly to changes in biotic and abiotic conditions, while ecosystem-level responses develop much more slowly (e.g., over months, seasons, years, or decades). To better understand the role of the slow responses in regulating interannual variability in NEE, we partitioned NEE into two major ecological terms—gross primary productivity (GPP) and ecosystem respiration (Reco). We tested a set of hypotheses on seasonal scales using the flux and environment data collected from 2000 to 2015 in an oak-grass savanna area in California where ecosystems experience a wet winter and spring and a five-month-long summer drought each year. In our results, the spring season (Apr.–Jun.) contributed more than 50% of annual GPP and Reco. An analysis of outliers showed that each season could introduce significant anomalies in annual carbon budgets. The magnitude of the contribution depends on biotic and abiotic seasonal circumstances across the year and the particular sequences. We found that: (1) extremely wet springs reduced GPP in the years of 2006, 2011 and 2012; (2) soil moisture left from those extremely wet springs enhanced summer GPP; (3) groundwater recharged during the spring of 2011 was associated with the snowpack depth accumulated during the winter between 2010 and 2011; (4) dry autumns (Oct.–Dec.) and winters (Jan.–Mar.) decreased Reco significantly; (5) grass litter produced in previous seasons might increase Reco, and the effect of litter legacy on Reco was more observable in the second year of two consecutive wet springs. These findings confirm that biotic and abiotic extremes and legacies can introduce variations to annual ecosystem carbon balance, other than those that might be explained by the fast responses.