A depth-discrete groundwater monitoring well is crucial to observing groundwater contamination and subsurface environments. To address this issue, we developed a multilevel monitoring system (MLMS). Because optical fiber sensors are small, have low voltage requirements, and have minimal signal loss over a long distance, we used fiber Bragg grating (FBG) technology to develop a MLMS to observe the depth-discrete aquifer status. The developed FBG sensors and MLMS were examined by a laboratory test and two field tests, respectively. The results show that the FBG piezometer and thermometer accuracies are 0.2% and 0.4% full-scale, respectively. The MLMS can be easily installed in a 2-inch well without a sealing process and can successfully measure the depth-discrete aquifer status at the selected fully-penetrated wells during the two injection events at the study site. The analysis of the collected data and their corresponding injection event reveals the possible structure of the subsurface hydraulic connections at the study sites. These results demonstrate that the FBG MLMS can be an alternative subsurface monitoring system, which has the advantage of a relatively low cost, good data collection efficiency, and environmental sustainability.