Groundwater modelling is an important management tool to study the behaviour of aquifer system under various hydrological stresses. Present study was carried out in deltaic regions of the Cauvery river, with an objective of estimating the minimum river flow required to improve the groundwater quality by numerical modelling. Cauvery river delta is the most productive agricultural plains of south India, but the agricultural activities during the last few decades have decreased due to limited flow in the river and increasing concentration of solutes in groundwater in the eastern parts. In order to understand the causes for increasing concentration, a three-layered finite-difference flow model was formulated to simulate the groundwater head and solute transport. The model was used to simulate the groundwater flow and solute transport for 5 years from July 2007 to June 2012. There was a fairly good agreement between the computed and observed groundwater heads. The chloride and nitrate ions were considered for solute transport modelling. Observed and simulated temporal variation in chloride and nitrate concentrations were comparable. The simulated solute concentrations from July 2007 to June 2012 showed an accumulation of solutes in groundwater of coastal part of the study area. The model was used to find the flow to be maintained in the river and rainfall recharge required to flush the ions into the sea. This can be achieved by maintaining minimal flow in the river and through regulation of fertilizer use as well as by creating awareness of sustainable use of groundwater in this area.