This paper describes the basic control, navigation, and mapping methods and experiments a hovering autonomous underwater vehicle (AUV) designed to explore flooded cenotes in Mexico as part of the DEPTHX project. We describe the low level control system of the vehicle, and present a dead reckoning navigation filter that compensates for frequent Doppler velocity log (DVL) dropouts. Sonar data collected during autonomous excursions in a limestone quarry are used to generate a map of the quarry geometry.