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There is a lack of understanding and methods for assessing the effects of anthropogenic disruptions, (i.e. river fragmentation due to dam construction) on the extent and degree of groundwater-surface water interaction and geochemical processes affecting the quality of water in semi-arid, coastal catchments. This study applied a novel combination of electrical resistivity tomography (ERT) and elemental and isotope geochemistry in a coastal river disturbed by extended drought and periodic flooding due to the operation of multiple dams. Geochemical analyses show that the saltwater barrier causes an increase in salinity in surface water in the downstream river as a result of limited freshwater inflows, strong evaporation effects on shallow groundwater and mostly stagnant river water, and is not due to saltwater intrusion by tidal flooding. Discharge from bank storage is dominant (similar to 84%) in the downstream fragment and its contribution could increase salinity levels within the hyporheic zone and surface water. When surface water levels go up due to upstream freshwater releases the river temporarily displaces high salinity water trapped in the hyporheic zone to the underlying aquifer. Geochemical modeling shows a higher contribution of distant and deeper groundwater (similar to 40%) in the upstream river and lower discharge from bank storage (similar to 13%) through the hyporheic zone. Recharge frombank storage is a source of high salt to both upstream and downstream portions of the river but its contribution is higher below the dam. Continuous ERT imaging of the river bed complements geochemistry findings and indicate that while lithologically similar, downstream of the dam, the shallow aquifer is affected by salinization while fresher water saturates the aquifer in the upstream fragment. The relative contribution of flows (i.e. surface water releases or groundwater discharge) as related to the river fragmentation control changes of streamwater chemistry and likely impact the interpretation of seasonal trends. (C) 2016 Elsevier B.V. All rights reserved.