The Indian River Lagoon (IRL) extends for 160 miles along Florida's east coast and is a complex system of three estuaries - Mosquito Lagoon, Banana River Lagoon, and Indian River Lagoon. Two concurrent phytoplankton blooms occurred in the IRL in 2011 that had detrimental ecological effects on the estuarine system. St. Johns River Water Management District (SJRWMD) is participating in a multi-agency effort to better characterize and understand the factors effecting algal dynamics of the IRL. The U.S. Geological Survey (USGS) worked in cooperation with the SJRWMD to study the spatial variability of water-quality conditions, especially conditions related to potential algal blooms, between sampling sites and the spatial extent of the influence of tributaries to IRL. To collect spatially dense water-quality data, the USGS used an autonomous underwater vehicle (AUV) that is capable of measuring water-quality data and bathymetric and side-scan sonar data in a spatially dense fashion - approximately once a second or every 3 feet. The AUV has a multi-parameter water-quality monitor equipped to collect water temperature, specific conductance, pH, dissolved oxygen, turbidity, total chlorophyll fluorescence, and phycocyanin (freshwater blue-green algae) fluorescence. This data release is for the fourteen water-quality surveys collected over the period from August of 2016 to November of 2017 - three in Banana River Lagoon, three in Mosquito Lagoon, and eight in Indian River Lagoon.