Lentic ecosystems are important agents of local and global carbon cycling, but their contribution varies along gradients of dissolved organic matter (DOM) and productivity. We investigated how contrasting summer and autumn precipitation can shape annual and inter-annual variation in ecosystem carbon (C) flux (gross primary production (GPP), ecosystem respiration (ER), and CO2 efflux) in two subtropical lakes differing substantially in trophic state and water color. Instrumented buoys recorded time series of free-water DO, terrestrial DOM (tDOM), chlorophyll a, water temperature profiles, and meteorological measurements over five years (2009–2011 and 2014–2015). Reduced precipitation caused immediate and prolonged effects on C flux in both lakes. During the drought year (2014) GPP and ER declined by 60 to 80% and both lakes were either CO2 sinks or neutral. In the subsequent wet year (2015), GPP and ER increased by 40 to 110%, and both lakes shifted to strong net CO2 emitters. Higher ecosystem R resulted from larger GPP while higher tDOM contributed to a dramatic increase in dissolved inorganic carbon, which intensified CO2 emission in both lakes. C flux was more responsive in the clear mesotrophic lake, declining by approximately 40% in the cumulative GPP and ER, and increasing by >400% in CO2 efflux whereas changes in the oligotrophic colored lake were more modest (approximately 30% and 300% for metabolic declines and efflux increases, respectively). Temporal variation and magnitude of C flux were governed by tDOM-mediated changes in epilimnetic nutrient levels and hypolimnetic light availability. This study demonstrated terrestrial loads of DOM strongly influence the inter-annual response and sensitivity of ecosystem C flux to variation in inter-annual precipitation. Our findings have important implications for predicting the trend, magnitude, duration, and sensitivity of the response of C flux in subtropical lakes/reservoirs to future changes in precipitation patterns under altered climatic conditions.