Seepage beneath artificial levees is a common concern during flooding events. Risk of levee failure is elevated when piping erodes channels beneath the levee, evidenced by the formation of sand boils where transported sediments discharge. Along the lower Mississippi River, pathways of floodwater beneath the levee vary with surface geology, following deeper paths where the levee overlies fine-grained channel-fill deposits, and shallower (higher risk) paths where it overlies sand-bar deposits. Shallow, organic-rich alluvial aquifers are often geochemically stratified into upper oxic and lower anoxic zones, raising the possibility of using the geochemical signatures of discharging water from sand boils to differentiate flow pathways. A preliminary investigation north of Vicksburg, MS, (USA) during the 2011 Mississippi River flood demonstrated the potential of using geochemistry to identify deep and shallow pathways, though the study was limited to cation and trace element analyses. Sampling during the 2015 and 2016 floods for temperature, conductivity, redox potential (Eh), dissolved oxygen (DO), major ions, trace elements, tritium, and stable isotope ratios of oxygen, hydrogen, and strontium, facilitated a greater understanding of the nature of flow and geochemical evolution of groundwater in this environment. Characteristics of deeper flow pathways (relative to shallow) included (1) lower Eh and higher Fe and As, reflecting anoxic conditions and high-Fe sediments, (2) proportional increases in Fe and HCO3, indicating reductive dissolution of Fe-oxyhydroxides, and (3) higher ratios of Ba/Ca and Sr/Ca, reflecting differences in the elemental composition of minerals with depth. Tritium results indicate that subsurface flow pathways are dynamic, shifting spatially with the rapid changes in hydraulic gradients during and between flooding events. Estimated residence times of groundwater discharging from sand boils and relief wells ranged from essentially zero (discharge of concurrent floodwater) up to a quarter century. Lower strontium isotope ratios (87Sr/86Sr) were observed in the aquifer relative to river water, though with no clear variation with flow depth. Oxygen and hydrogen isotope ratios (δ18O and δ2H) show evidence of partial evaporation prior to recharge, also with no apparent variation with subsequent flow depth.