The data set includes temperature data from the base of the water column and below the bottom of the Indian River Lagoon, Brevard County, Florida. Data were collected near Eau Gallie, Melbourne, Florida and Riverwalk Park, Rockledge, Florida, on the western shore of the Lagoon. These data will ultimately be used to evaluate groundwater seepage. Data collection includes, temperature profiling using temperature stakes and distributed temperature sensing. Temperature stakes consist of 4 to 5 temperature sensors imbedded in 0.6 to 0.9 meter long polyvinyl chloride stakes that are designed to be driven into the sediment at the bottom of the lagoon. Sensors provide a time series of temperature in the sediments at several depths beneath the bottom of the lagoon. The variations in the temperature profile with depth can be modeled to evaluate groundwater seepage. The locations of these stakes are provided in geographic information system files, and the raw and final data from the individual stakes are provided. The initial release includes data from 8 stakes deployed on March 22, 2017 and retrieved on April 28, 2017. Distributed temperature sensing was conducted from May 23, 2017 to May 30, 2017. Distributed temperature sensing was conducted by sending light through a fiber optic cable that had been deployed on the bottom of the lagoon. The light refracted back to a sensor is dependent on the temperature of the cable. The deployed cables were about one kilometer (0.62 mile) long. This method provided temperatures measured every 20 minutes for each meter (3.3 feet) of the fiber-optic cable. The coordinates of the cable were determined using a hand-held geographic positioning system unit. The geospatial temperature data are provided through spreadsheet, comma delimited, and geographic information system files. Raw data files from the distributed temperature sensing instrumentation are also provided. These data were used to help guide the deployment of the temperature stakes.