As the Nairobi–Malaba Railway traverses the East African Rift Valley, it has complex engineering geological conditions due to the development of its geological formations. Since March 2018, four large ground fissures have occurred in the East African Rift Valley area crossed by the Nairobi–Malaba Railway engineering construction, posing a significant threat to the safety of the railway engineering. According to the field investigation, it is initially considered that the ground fissures are caused by the loss of strength of the lower soil layers. In view of the fact that the settlement occurred during the rainy season and no earthquake events were recorded in the local and nearby areas during that period, it is inferred that the ground fissures originated from the subduction of the underlying soil layer by the submerged erosion of groundwater. For this reason, a further field investigation was conducted and a geological trench was directly excavated to the underlying rock for the uneven ground settlement, which revealed that the overlying soil layers are mainly silty clay layers and volcanic ash layers, and there are some deep and long cracks of a certain width on the underlying volcanic rock layer and there is gas flow spilling from the cracks. The field investigation also found the existence of some penetrating holes in the volcanic rock layer and caves beneath the volcanic rock layer. Based on the field investigation and phenomenological analysis, it is concluded that during the rainy season, the alternating action phenomenon of downward seepage of water in the surface soil layer and upward reflux of water beneath the volcanic rock layer happened through the cracks and penetrating holes on the volcanic rock layer, and the alternating effect of groundwater flow causes some silty clay and volcanic ash particles to flow into the caves and cracks beneath the volcanic rock layer, which leads to the generation of ground fissures. In addition, to further confirm the reliability of this interpretation of the generative mechanism of ground fissures, related results of conventional geotechnical tests on the overlying soil were studied, which verified the conclusion obtained.