Chemical properties of lake water can provide valuable insight into its ecology. Lakes that are permanently frozen over with ice are generally inaccessible to comprehensive exploration by humans. This paper describes the integration of several novel and existing technologies into an autonomous underwater robot, ENDURANCE, that was successfully used for gathering scientific data in West Lake Bonney in Taylor Valley, Antarctica, in December 2008. This paper focuses on three novel technological and algorithmic solutions. First, a robust position estimation system that uses an acoustic beacon to complement traditional dead-reckoning is described. Second, a novel vision-based docking algorithm for locating and ascending a vertical shaft by tracking a blinking light source is presented. Third, a novel profiling system for measuring water properties while causing minimal water disturbance is described. Finally, experimental results from the scientific missions in 2008 in West Lake Bonney are presented.