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3D stacked circuits reduce communication delay in multicore system-on-chips (SoCs) and enable heterogeneous integration of cores, memories, sensors, and RF devices. However, vertical integration of layers exacerbates the reliability and thermal problems, and cooling is a limiting factor in multi-tier systems. Liquid cooling is a highly efficient solution to overcome the accelerated thermal problems in 3D architectures; however, liquid cooling brings new challenges in modeling and runtime management. This paper proposes a novel controller for improving energy efficiency and reliability in 3D systems through liquid cooling management and dynamic voltage frequency scaling (DVFS). The proposed fuzzy controller adjusts the liquid flow rate at runtime to match the cooling demand for preventing energy wastage of over-cooling and for maintaining a stable thermal profile. The DVFS decisions provide chip-level energy savings and help balancing the temperature across the system. Experimental results on 8- and 16-core multicore SoCs show that the controller prevents the system to exceed the given threshold temperature while reducing cooling energy by up to 50% and system-level energy by up to 21% in comparison to using a static worst-case flow rate setting.