Groundwater responses measured from multiple wells at different depths are essential for delineating the aquifer heterogeneity using hydraulic tomography (HT). In general, conducting HT requires many wells because traditional well monitoring is usually partially open at a specific depth interval or is fully penetrating. Accordingly, conducting an HT survey is typically costly and time-consuming. To tackle these issues, a new multi-level monitoring system (MLMS) for the HT survey was developed using the fiber Bragg grating (FBG) technique. This FBG MLMS could collect the depth-discrete groundwater observations from a fully penetrated 2-inch well. Three field campaigns were conducted to validate the capability of the FBG MLMS for HT surveys. The results show that the accuracy and stability of this MLMS are reliable and that FBG MLMS is beneficial for conducting an HT survey. Specifically, compared to the traditional monitoring well in an injection event, this FBG MLMS can concurrently cause an increase in the number of cross-hole tests several times and collect many more head observations than the standard methods, resulting in the observed flow fields efficiently reaching ergodic conditions and effectively improving the accuracy of the estimated hydraulic heterogeneity. Therefore, the FBG MLMS could be an alternative MLMS for efficiently and economically conducting an HT survey.