In groundwater modeling studies, accurate spatial and intensity identification of water sources and sinks is of critical importance. Precise construction data about wells (water sinks) are particularly difficult to obtain. The collection of well log data is expensive and laborious, and government records of historic well log data are often imprecise and incomplete with respect to the precise location or pumping rate. In many groundwater modeling studies, such as groundwater quality assessments, a precise representation of the horizontal and vertical distribution of well screens is required to accurately estimate contaminant breakthrough curves. The number of wells under consideration may be very large, for example, in the assessment of nonpoint source pollution. In this paper, we propose an imputation framework that allows for proper reconstruction of missing well data. Our approach exploits available information and tolerates data gaps and imprecisions. We demonstrate the value of this method for a subregion of the Central Valley aquifer (California, USA). We show that our framework imputes missing values that preserve statistical properties of available data and that remain consistent with the known spatial distribution of well screens and pumping rates in the three-dimensional aquifer system.