Understanding patterns in trace element concentrations and water quality within river systems provides a foundation to evaluate retrospective movements and habitat use of fish. Because trace elements are incorporated into calcified structures of fishes relative to water concentrations, baseline maps have application for fisheries management, including for rare species such as sturgeons. Therefore, trace elements [strontium (Sr), barium (Ba), manganese (Mn), zinc (Zn), and magnesium (Mg)], strontium isotopes ( 87 Sr/ 86 Sr), dissolved oxygen and salinity were measured in the Pearl River and Lake Pontchartrain watersheds, within Mississippi and Louisiana, USA for application in assessing riverine use by Gulf Sturgeon Acipenser oxyrinchus desotoi. Water samples were collected during the summerfall period when juvenile Gulf Sturgeon were anticipated to be present and analyzed by solution and multi-collector inductively coupled plasma mass spectrometry. Trace element to calcium (Ca) ratios in Sr, Ba, Zn, and Mg were distinguishable between the upper Pearl River and the Bogue Chitto River tributary, and the upper Pearl River and lower Pearl River. For most trace elements and 87 Sr/ 86 Sr, there was a gradual increase from upper river regions to lower river regions, and large differences between freshwater and saline areas. Lake Pontchartrain watershed rivers were not easily differentiated, but regions of low dissolved oxygen concentrations in the lower reaches suggest available Gulf Sturgeon habitat may be seasonally limited. Therefore, maps of water microchemistry in the Pearl River watershed allow for retrospective analyses of fish watershed use.