High-resolution topographic surveys were conducted at two pools on the Carmel River between 2014 and 2019 using a survey-grade total station. The Dam Reach pool (DMPOOL) is located within the Dam Reach, approximately 450 meters downstream of the former site of the San Clemente Dam. The Sleepy Hollow pool (SHPOOL) is located within the Sleepy Hollow reach, approximately 2.25 kilometers downstream of the former site of the San Clemente Dam. Both pools were surveyed in 2014, 2015, 2016, 2017, and 2019 using a total station, in conjunction with the channel cross-section surveys also conducted as part of this study (see accompanying file within this data release for topographic survey transect data). For the 2015 survey, a kayak-mounted single-beam echosounder was also used to augment the data collected with the total station. Horizontal and vertical coordinates are provided for each point surveyed. Vertical coordinates are referenced to the NAVD88 vertical datum, in units of meters. Horizontal coordinates are referenced to the NAD83(2011) reference frame, projected in Universal Transverse Mercator (UTM) coordinates (zone 10N), in units of meters.