During the development of urban underground space, ground subsidence triggered by legacy coal mine goafs poses a severe threat to the safety of rail transit engineering. Taking the Shengjing mining area traversed by Jinan Metro Line 8 as the study area, this paper aims to construct an integrated research framework encompassing refined geophysical detection, comparative multi-method settlement analysis, and fluid-solid coupling numerical simulation. The objective is to provide a theoretical basis for deformation risk assessment and anti-deformation design of urban rail transit in water-rich mining areas.A comprehensive geophysical strategy, primarily utilizing the Transient Electromagnetic Method (TEM), was applied to delineate the distribution of water-filled goafs, the reliability of which was verified by five boreholes. Subsequently, the Probability Integral Method (PIM) and FLAC3D three-dimensional numerical simulation were employed to calculate and compare the surface settlement caused by the No. 3 and No. 9 coal seam goafs. The 3D numerical model systematically accounted for the lithological differences of 22 strata and the weakening effects of faults. Furthermore, fluid-solid coupling simulations were conducted under two scenarios: dry season (groundwater depth of 50 m) and wet season (groundwater depth of 20 m), to quantitatively evaluate the impact of groundwater level fluctuations on subsidence.(1) TEM clearly identified a "high-low-high" three-layer geoelectric structure, and the delineated low-resistivity anomaly zones were highly consistent with the water-filled goafs revealed by drilling. (2) The maximum surface settlement predicted by PIM was 864.12 mm, whereas the FLAC3D result was 915.3 mm. PIM carries a risk of systematic underestimation as it fails to account for the overlapping disturbance of multiple seams and fault activation. The numerical simulation also revealed that the F11 fault causes discontinuous deformation, and multi-seam mining transforms the floor of the upper coal seam from heaving to settling. (3) Groundwater significantly intensifies subsidence: compared to the dry condition, the maximum surface settlement increased by 9.96% (reaching 1006.5 mm) in the dry season and by 32.3% (reaching 1210.9 mm) in the wet season. The primary controlling mechanism is the increase in total stress on the rock mass due to elevated pore water pressure.It is recommended that PIM and numerical simulation be used jointly for mutual verification. This study quantified the reactivation weight of groundwater on legacy goafs, addressing the limitations of traditional empirical formulas in water-sensitive strata. The findings provide a scientific reference for settlement prediction and safety evaluation of similar underground engineering projects in water-rich mining areas.