Water-quality samples were collected quarterly during 1994-99 from 604 wells screened in the surficial aquifer system beneath the Charleston Naval Complex, North Charleston, South Carolina. Arsenic and thallium were selected for analysis because concentrations of these metals in some wells consistently exceeded the established (2001) drinking water maximum contaminant levels of 10 and 2 micrograms per liter, respectively. The analysis was conducted to determine the magnitude and spatial distribution of arsenic and thallium in ground water at the Charleston Naval Complex and to quantify arsenic and thallium concentrations in a dated sediment core from Shipyard Creek marsh near the southern boundary of the Naval Complex. The surficial aquifer system beneath the Charleston Naval Complex consists of an unconfined upper surficial aquifer and a confined lower surficial aquifer. Hydraulic connection between the two aquifers is limited or nonexistent throughout the system at the Naval Complex. The Charleston Naval Complex is divided into nine operational units designated as zones A through I. Arsenic and thallium concentration data were compiled and interpreted for the two surficial aquifers within each zone. Mean arsenic (n=603) and thallium (n=604) concentrations were calculated for water samples from each well screened in the upper and lower surficial aquifers. In the upper surficial aquifer, mean arsenic concentrations ranged from 0.9 to 339 micrograms per liter and exceeded 10 micrograms per liter in 29 percent of the wells. In the lower surficial aquifer, mean arsenic concentrations ranged from 1.0 to 97.4 micrograms per liter and exceeded 10 micrograms per liter in 23 percent of the wells. The greatest number of water samples with mean arsenic concentrations exceeding 10 micrograms per liter were collected from wells in the upper surficial aquifer at zone E in the northwestern part of the study area. Well clusters, defined as three or more wells in a solid-waste management unit or area of concern, where the mean arsenic concentration exceeded 10 micrograms per liter, were identified in association with 12 sites in the upper surficial aquifer-solid-waste management unit 039 (a drum-storage area) in zone A; solid-waste management units 044 (coal-storage area) and 047 (burning dump) in zone C; solid-waste management unit 065 (lead-storage area) and area of concern 556 (dry docks 3 and 4) in zone E; areas of concern 609 (building 1346 gas station) and 613 (locomotive shop) in zone F; solid-waste management units 006 (public works storage yard) and 008 (oil sludge pit), and area of concern 709 (fuel-delivery system wells 12, 13, and 14) in zone G; and solid-waste management units 009 (closed landfill) and 196 (south landfill) in zone H. One well cluster was identified in the lower surficial aquifer in association with solidwaste management unit 009 (closed landfill) in zone H. Mean thallium concentrations in water from all wells ranged from less than 1.6 to 32.6 micrograms per liter in water samples from the upper surficial aquifer, and from less than 1.6 to 67.7 micrograms per liter in water samples from the lower surficial aquifer. Mean thallium concentrations equal to or greater than 10 micrograms per liter were present in water samples from 21 of 604 wells (3.5 percent). Of the 21 wells, 14 wells were located at solid-waste management unit 009 (closed landfill) in zone H near Shipyard Creek, 8 wells in the upper aquifer, and 6 wells in the lower aquifer. One well cluster where thallium exceeded 10 micrograms per liter was identified in association with solid-waste management unit 009 (closed landfill) in the upper surficial aquifer. Mean arsenic and thallium concentrations in water were calculated for all wells screened in one aquifer and located in a single zone, and are referred to as zone mean concentration in this report. Zone mean arsenic concentrations in all nine zones ranged from 3.2 to 18 micrograms per liter in water samples from the upper surficial aquifer and from 2.7 to 22 micrograms per liter in water samples from the lower surficial aquifer. Zone mean thallium concentrations in all nine zones ranged from 3.2 to 13 micrograms per liter in water samples from the upper surficial aquifer and from 3.2 to 14 micrograms per liter in water samples from the lower surficial aquifer. Ground-water samples rarely had elevated (equal to or greater than 10 micrograms per liter) concentrations of both arsenic and thallium. Water samples had coincident elevated arsenic and thallium concentrations in 10 wells in zone H, 1 well in zone A, and 1 well in zone B. Sediment quality at Shipyard Creek marsh was investigated by collecting an 11.8-foot -long sediment core (SYC-1) adjacent to zone I. The mean arsenic concentration in sediment samples from SYC-1 (n= 160) was 3.05 milligrams per kilogram plus or minus 0.92. The mean arsenic concentration and standard deviation calculated for SYC-1 sediment samples fall within the standard error for the background mean arsenic concentration reported for South Carolina sediments (1.5 milligrams per kilogram plus or minus 2. 7). All but one sample (core depth =50 inches) was less than the threshold-effects level of 7.24 milligrams per kilogram. Acid extracts of the sediment samples were analyzed for thallium concentration, but none were detected. These data indicate no obvious change in arsenic or thallium concentrations with depth in the core.