This paper investigated the hydrodynamics, spatio-temporal variability of temperature/salinity and the residence time of tracer concentrations in a largest brackish water coastal lagoon in Asia, namely the Chilika lagoon, India. An integrated approach combined the measurement and 2D hydrodynamic-advection/dispersion model is used to simulate circulation and temperature/salinity, and estimated the water residence time in lagoon under different forcing mechanisms, such as tide, wind and freshwater discharge during the dry and wet periods. Water circulation inside the lagoon is simulated when wind is included with the tide only forcing during dry period, and freshwater influx is included with the tide and wind forcing during wet period. Under the realistic forcing conditions, the computed temporal variability of water temperature and salinity are well correlated with the measurements in both the periods. The spatial variations of water temperature within the lagoon is influenced by the meteorological conditions, tide and freshwater influx as well as the shallowness of the lagoon, whereas the salinity is spatially controlled by the freshwater influx from the riverine system and seawater intrusion through the tidal inlets. The numerical model results show that in the Chilika lagoon tidal and river influx affect significantly the residence time spatially, and is site specific. The residence time varies from values of 4–5 days in the outer channel (OC) and 132 days at the northern sector (NS) in the main body of lagoon. The current study represents a first attempt to use a combined model approach, which is therefore, a useful tool to support the ecological implication of the lagoon ecosystem. •Hydrodynamics and residence time is investigated under different scenarios.•A 2D hydrodynamic-AD model is used for model simulations with observations.•Temperature/salinity distribution mainly controlled by tidal and river inflows.•Spatially heterogeneous residence time, and is site specific that varies seasonally.