Paleo-climatic induced sedimentation controls present-day recharge and the fresh-salt groundwater distribution in Quaternary delta systems. During sea-level highstands, marine clays, with saline pore water, were deposited, and are interbedded with aquifers of coarse-grained sandy fluvial and shallow marine deposits, laid down during lowstands. The low-permeable marine layers may inhibit recent recharge to deeper aquifers, and thereby limit sustainable use of these freshwater resources. This phenomenon has been investigated in the Red River delta plain, using geophysical borehole logging, transient electromagnetic soundings, groundwater chemistry, stable isotope analysis and 3H and 14C dating of groundwater. Results reveal that marine saline pore water is still present in the Holocene marine clays, implying that fresh water has not entered the clays since their deposition. Therefore, recharge within the delta plain is not occurring and the deeper aquifers are hydraulically disconnected from the upper sandy layers. Today, recharge only occurs from the hinterland. Recharge during the last glacial period has flushed salt pore water from Pleistocene marine clays, but these clays were again affected by saline water during the Holocene transgression. The use of the groundwater resources in the delta plain must be adjusted to the present recharge to be sustainable.