Vertical hydraulic gradient (VHG) provides detailed information on 3D groundwater flows in alluvial fans, but its regional mapping is complicated by a lack of piezometer nests and uncertainty in conventional well data. Especially, determining representative depth of well screen in each well is problematic. Here, a VHG map of the Toyohira River alluvial fan, Sapporo, Japan, is constructed based on groundwater table elevation (GTE), using available well-data of various screen lengths and depths. The water-level data after 1988, when subway constructions are mostly completed in the city, are divided into those of shallow wells (≤20 m deep), and those of deep wells (>20 m deep). First, the GTE map is generated by kriging interpolation of shallow well data with topographic drift. Next, the individual VHG value of each deep well is calculated using its top, middle, and bottom elevations of the screen depths, respectively. The VHG maps of three cases are then obtained using neighborhood kriging. The VHG map of the bottom screen depths has proven most valid by cross-validation. The VHG map better visualizes that downward flows of groundwater are predominant over the fan. Positive area of VHG is mostly vanished around the fan-toe, indicating urbanization effect such as artificial withdrawals. A negative peak of VHG corresponds to recharge area, and is seen along the distinct losing section in the river. The negative peak also expands upstream to the fan-apex where a basement is suddenly depressed.