This paper presents results from the integration of a compact quantum magnetometer system and an agile underwater glider for magnetic survey. A highly maneuverable underwater glider, ROUGHIE, was customized to carry an increased payload and reduce the vehicle’s magnetic signature. A sensor suite composed of a vector and scalar magnetometer was mounted in an external boom at the rear of the vehicle. The combined system was deployed in a constrained pool environment to detect seeded magnetic targets and create a magnetic map of the test area. Presented is a systematic magnetic disturbance reduction process, test procedure for anomaly mapping, and results from constrained operation featuring underwater motion capture system for ground truth localization. Validation in the noisy and constrained pool environment creates a trajectory towards affordable littoral magnetic anomaly mapping infrastructure. Such a marine sensor technology will be capable of extended operation in challenging areas while providing high-resolution, timely magnetic data to operators for automated detection and classification of marine objects.