Sedimentological, malacological, and pollen analyses from 14C-dated alluvial sections from the Luján River provide a detailed record of environmental changes during the Holocene in the northeastern Pampas of Argentina. From 11,200 to 9000 14C yr B.P., both sedimentary and biological components suggest that the depositional environment was eutrophic, alkaline, and freshwater to brackish shallow water bodies without significant water circulation. During this time, bioclastic sedimentation was dominant and the shallow water bodies reached maximum development as the climate became more humid, suggesting an increase in precipitation. Short-term fluctuations in climate during the last stage of this interval may have been sufficient to initiate changes in the water bodies, as reduction of the volume alternated with periods of flooding. The beginning of the evolution of shallow swamps in the wide floodplain or huge wetlands was contemporaneous with a sea level lower than the present one. From 9000 and 7000 14C yr B.P., mesotrophic, alkaline, brackish, probably anoxic swamps existed. Between 7000 and 3000 14C yr B.P., anoxic calcareous swamps were formed, with subaerial exposure and development of the Puesto Berrondo Soil (3500–2900 14C yr B.P.). A trend to a reduction of water bodies is recorded from 9000 to ca. 3000 14C yr B.P., with a significant reduction after ca. 7000 14C yr B.P. A shift to subhumid–dry climate after 7000 14C yr B.P. appears to be the main cause. During this time, an additional external forcing toward higher groundwater levels was caused by Holocene marine transgression causing changes in the water bodies levels. The climate became drier during the late Holocene (ca. 3000 yr B.P.), when clastic sedimentation increased, under subhumid–dry conditions. Flood events increased in frequency during this time. From ca. A.D. 1790 to present, the pollen record reflects widespread disturbance of the vegetation during the European settlement.