An ancient, brackish, anoxic, and relatively hot water body exists within the Yarqon-Tanninim Aquifer in southern Israel. A hydrogeological-geochemical conceptual model is presented, whereby the low water quality is the outcome of three conditions that are met simultaneously: (1) Presence of an organic-rich unit with low permeability that overlies and confines the aquifer; the confining unit contains perched horizons with relatively saline water. (2) Local phreatic/roofed conditions within the aquifer that enable seepage of the organic-rich brackish water from above. The oxidation of the dissolved organic matter in the seeping water consumes the dissolved oxygen and continues through bacterial sulfate reduction, with H S as a product. These exothermic reactions result in some heating. (3) The seeping water comprises a relatively large portion of the water volume. In the presented case study, the latter condition first developed in the Late Pleistocene following climate change, which led to a dramatic decline in recharge. Consequently, water flow in the local basin has nearly ceased, as evident by old water ages, specific isotopic composition, and nearly equipotential water levels. The continuous seepage from above into the almost stagnant water body has resulted in degraded water quality. Seepages of organic-rich brackish water exist at other sites throughout the aquifer but have limited impact on the salinity and redox conditions due to the dynamic water flow, which flushes the seeping water, that is, the third condition is not met. The coexistence of the above three conditions may explain the development of anoxic and saline groundwater in other aquifers worldwide.