A 2,250 mm whirlpool foundation pit is located in Donghai Island, Zhanjiang City, Guangdong Province, China. The layers of the island are composed of multi-aquifers and multi-aquitards (MAMA). The aquifers are intersected by partial aquitard lenses. A large confined aquifer is frequently interbedded and separated into several sub-confined aquifers by partial aquitards. In the 2,250 mm foundation pit, the water level of two confined aquifers was reduced to satisfy excavation requirements and prevent water inrush. Construction of the 32.55 m deep foundation pit encountered MAMA and potential defects of the diaphragm wall. The pumping wells in the second confined aquifer were used to reduce the water level to ensure the safety of bottom excavation. The pumping wells in the first confined aquifer were used to reduce the water level under emergency conditions to prevent potential water inrush and piping from the defects of the diaphragm wall. Field pumping tests and numerical simulations were performed to determine the risk of leakage and verify the capability of the pumping wells to reduce the water level. Quicksand occurred during shallow excavation because of leakage although the confined aquifer had been cut off and pumped for a long time. Three pumping wells were installed to reduce the water level. When the foundation pit was excavated to a depth of 24 m, water inrush occurred at the middle of the pit bottom although the water level of the dewatered aquifer had been reduced to below the excavation face. A 90 m deep borehole was found where the underlying confined aquifer below the first aquifer induced the water inrush. Although the upper water level was reduced, the high water level in the deep part still induced water inrush. The pumping wells in the second aquifer were all opened, and the water level of the underlying confined aquifer was reduced. After the water level was reduced to below the pit bottom, the borehole was filled, and the water inrush stopped. However, water inrush occurred on the cracks of the diaphragm wall as predicted. The pre-installed pumping wells were opened to control the water inrush. The deepest foundation pit on the island was constructed successfully after dealing with the water inrush and leakages.