The Groundwater Resource Section (GRS) identifies, assesses and protects the city's groundwater resources from degradation by operating regulatory programs in well permitting and wellhead protection. The GRS obtains its direct authority from Chapter 366 of the City Ordinance Code and Environmental Protection Board (EPB) Rule 8.

GRS program responsibilities include the following: Permitting and inspection of the construction, repair, modification, and abandonment of water wells; Evaluation of the potential risk to Public Supply Wells based on contamination sites and private wells within Wellhead Protection Areas (WHPAs); and public education on groundwater resources. Cooperative efforts between the GRS and other governmental agencies include programs to address salt water intrusion, groundwater contamination and other resource threats. The GRS also leads the way within the Environmental Quality Division regarding the application and use of Geographic Information System (GIS) technology. The GRS maintains a county-wide well inventory GIS database as well as a groundwater contamination risk management GIS application that includes documented groundwater contamination discharge sites across Duval County.

A top priority for the GRS is the protection of the city’s primary potable water supply, the Floridan Aquifer. However, the program has grown to include protection of all of Jacksonville’s available aquifers and to encourage the use of alternative water sources such as reclaimed wastewater for irrigation.