Basing on long-term observation data, we employed a three-dimensional environmental model to analyze the hydraulic retention effect on the net ecosystem production (NEP) of two shallow montane lakes. Our results strongly suggest that Tsui-Fong Lake (a mesotrophic lake) is substantially higher in both NEP and carbon sink functions than Yuang-Yang Lake (an oligotrophic lake). We conclude that typhoon-induced mixing plays a critical role in controlling the NEP and carbon sinks in Taiwan shallow subtropical lakes.