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Interaction between surface water and groundwater is an important component of the water cycle that affects the physicochemical and biological characteristics of lakes, streams, wetlands, and seacoasts. Due to the complex interaction of geologic, topographic, and hydrologic factors, flow between lakes and groundwater remains poorly understood. Evolution of conceptual models over the past 30 years describes processes of advection, dispersion, and free convection that occur in different lake flow regimes. Few detailed field studies document the validity of these conceptual models because of the difficulty of studying the subsurface and the prohibitive cost of instrumenting large areas. In the semi-arid Western Nebraska Sand Hills, the largest dune field in the Western Hemisphere, more than 1,600 permanent shallow groundwater-fed endorheic lakes have salinity ranging from 0.3 to over 100 g/L. Shallow plumes from saline lakes discharging into the relatively homogenous and fresh groundwater aquifer serve as a unique and excellent example for studying lake-aquifer interactions. This study investigates the processes contributing to spatial and temporal variability of lake salinity in the Sand Hills. Methods in this study combine the use of terrain analysis, electromagnetic and resistivity imaging geophysics, hydraulic testing, lakebed dating using 14C and optically stimulated luminescence, hydro-chemical analysis, and salt crust and dust collection. An analysis of surface and sub-surface topography of the Western Nebraska Sand Hills illustrates how the pre-existing topography of the top of the Ogallala Group, together with dune blockage events, resulted in the formation of hundreds of lakes with highest carbonate saline waters in North America. A detailed field study shows the complex interaction of discharge and flow-through regimes, overland flow, and free convection and how they affect the lake salt balance. Finally, the concept of groundwater-land surface-atmosphere "salt conveyor", where evaporative concentration of fresh groundwater allows saline lakes to precipitate salt crusts along their shore and emit dusts is also introduced as an important mechanism that plays an important, albeit often unappreciated, role in the salt balance.