Tidal estuaries support everyday functions for over 80% of Australia's population living within 50 km of the coastline and thus come under immense pressure of physicochemical changes. Most studies in estuarine applications have used the bed roughness as the single calibration parameter to calibrate hydrodynamic modelling, yet errors in bathymetric data can significantly impose uncertainties into the model outputs. In this study, we evaluated the sensitivity of a hydrodynamic model of a micro-tidal estuary to both the bed roughness and bathymetry offset through comparing observed and modelled water level and velocity. Treating both bathymetry offset and bed roughness as calibration parameters, three calibration scenarios were tested to examine the impact of these parameters. To validate the model, Lagrangian drifter data as a new dataset in shallow estuaries were used. The analysis shows that model outputs are more sensitive to the variation of bathymetry offset than bed roughness. Results show that calibrating the bathymetry offset alone can significantly improve model performance. Simultaneous calibration of both parameters can provide further improvement, particularly for capturing the water level. Drifter and modelled velocities are highly correlated during flood tides, whereas the correlation is low for slack water because of wind-induced current on drifters.