This dataset contains the data points collected during the bathymetric survey of Lago Caonillas between September and November 2012 by U.S. Geological Survey. The 2012 bathymetric survey was conducted using a bathymetric/land survey system, consisting of a global positioning system (GPS) coupled to a digital depth sounder. A total of 155 survey navigation lines were established at 50 meter (m) intervals, beginning at the dam and continuing upstream along the river branches of the reservoir. Geographic position (accuracy of less than 2 m) and water depths (accuracy of 2 centimeters [cm] ±1 percent of the measured depth) were acquired simultaneously using the GPS interfaced to the depth sounder. The fathometer was calibrated prior to each day of survey by using a bar check. Data points collected on September 2012 for Lago Caonillas were adjusted to represent depth relative to the spillway elevation (251.76 meters above mean sea level). However, data collected during November 2012 was not adjusted since the water elevation at the reservoir was at the crest of the spillway structure. The reservoir pool elevation was monitored at the continuous recording USGS lake-level monitoring station 50026140 Lago Caonillas at damsite near Utuado, Puerto Rico. Lago Caonillas is owned and operated by the Puerto Rico Electric Power Authority (PREPA) since 1996. Because of the importance of Lago Caonillas to the North Coast Superaqueduct, the U.S. Geological Survey (USGS), in cooperation with PRASA, conducted a sedimentation survey of Lago Caonillas between September and November 2012 to update estimates of the reservoir’s storage capacity.