The two-tank water system is common practice for the storage and distribution of water in many homes. Water is transported via a pipeline network from the storage tank (lower tank) to the distribution tank (overhead tank) using an electric pumping machine. Due to limited control in the existing pumping system, water wastage becomes inevitable. Determining the quality of water in the overhead tank before supply in the home is still unaddressed. In this work, an integrated Android mobile App and a control system were developed to assess the water quality, perform level check in the overhead tank, and activate intelligent pumping control. An ultrasonic pulse-echo technique was used for water level checks, while the water turbidity and pH signals were used for water quality checks. Three-level control conditions (LC_1, LC_2, LC_3) and two water quality check conditions (QC_1 and QC_2) were devised and used in the intelligent control algorithm of the system. Control valve1 regulates the flushable poor water quality while valve2 regulates the house's supply of good water quality. The absolute relative error between the expected time and the system time of filling the tank level was observed to be less than 10% when the water volume is less than 81%. Hence, distortion in the sensory signals increases and worsen as the water level approaches the ultrasonic sensor position. The poor internet signal network was observed to affect the real-time monitoring and automation of the system control through delay in system responses to commands. However, the average recorded response time of the system is 3 s, and it could be less in the situation of good internet network services.