Abstract This study proposes a novel comprehensive hydrodynamic flood modelling framework over Mithi river watershed in Mumbai, India, a coastal urban area, to reduce the inundation extent by incorporation of different inland hydraulic scenarios. First, the study addresses the issue of data scarcity by adapting alternate robust techniques to estimate design rainfall, tidal elevation and discharge, the key inputs for a flood model. Following that, a three-way linked flood model has been developed in the MIKE FLOOD platform, considering river, stormwater, overland flow and tidal influence to generate flood inundation and subsequently hazard maps for various inland hydraulic scenarios, by incorporating different feasible cross-sections and lining materials. The flood inundation and hazard maps have been derived for 10-, 50- and 200-year return periods of design rainfall, discharge and tide to identify the best possible flood-reducing hydraulic scenario. It is observed that a ‘trapezoidal river cross-section lined with concrete’ relatively maximizes the reduction in flooding extent. The proposed framework can be implemented as an effective flood mitigation strategy in data-scarce, densely populated and space-constrained areas.