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Lacustrine sedimentary deposits are a primary archive of terrestrial paleoclimatic information, and groundwater fluxes under arid climates can dominate water budgets in lake and playa environments. In this paper, we investigate the effects of basin-scale water table fluctuations on lacustrine paleoclimatic records in and regions using the hydrogeologic model MWT3D. Boundary conditions for paleo-recharge over the past 57 ka, land surface topography, the location of lakes, and subsurface geology were based on information available for a 600-km cross section across the western Murray Basin, Australia. Results indicate the importance of the physical interaction between the water table and the land surface in controlling the location and the timing of formation of paleoclimatic lacustrine records. Lakes in different positions across the watershed preserved different records of climate (wet versus dry), although the same recharge history was applied. Changes in groundwater seepage to the surface lagged behind the climatic signal between 500 and 220 years across the basin. The size of the flow system, specifically the distance from the local discharge point to the adjacent groundwater divide, was the primary control on the time lag. With large fluctuations in water table elevation (>50 m) this distance changes considerably from wet to dry climatic conditions. Our results are largely consistent with observed paleoclimatic records derived from lakes across the Murray Basin.