First, let me verify the model. You say, "Master Liquid 120L". On the Cooler Master website there are several models with similar names. I looked up the one called "MasterLiquid Lite 120", which is different from their "MasterLiquid 120" and their models that include LED lighting. So that Lite model is what I basing this on. Unfortunately, the manual for this cooler system says absolutely nothing about the electrical connections to be used.
From what I can see, the design is intended to work this way. The pump has a cable ending in a 3-pin fan connector. I'm pretty sure it has only two functions. It gets a constant 12 VDC power supply from a mobo header so that it always runs at full speed. And it returns the pump's speed signal to the mobo to be monitored for failure. So this should plug into the mobo SYS_FAN2 header that supplies constant 12 VDC with no attempt to control it. HOWEVER, the manual indicates that this header does NOT accept the speed signal and monitor it, so YOU will need to verify from time to time that the pump is working.
The cooler system comes with a 4-pin PWM fan for the radiator. The intent is that this fan's speed will be under automatic control based on the CPU chip's internal temperature, and all control of CPU cooling will be done by manipulating the speed of the radiator fan. So, plug this fan into your CPU_FAN header and it will do that job.
That leaves the mobo's 4-pin SYS_FAN1 header available for PWM-style fans to cool the case. I expect that is what it is doing already.