The physical scenarios and model setup included in this repository were used to perform numerical simulations to analyze the role of convergence and short-duration river pulses on salinity distribution in idealized alluvial estuaries. The simulations were performed with a 3D implementation of the Delft 3D model. Short description of the included files. Scenarios.zip: Zip file containing the physical scenarios in which the salinity distribution and the dynamic response after river pulses were analyzed. Grid files (.grd, .enc) and depth files (.dep) for each scenario (scenario 1 - scenario 5) are included. Flow.zip: zip file containing the files necessary to run the 10-day Delft 3D simulation (flow module) included in the first set of numerical experiments (high river flow conditions under constant tide-river flow phase). The simulation is related to scenario 3 under the intermediate river discharge hydrograph. Supplementary information (Supplementary_info.pdf) contains geometry details and results from the sensitivity analysis. The research leading to this numerical setup was funded by the Spanish Ministry of Economy and Competitiveness, Project PID2021-125895O/AEI /10.13039/501100011033/FEDER, UE. The work of the first author received funding from the program Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2021), Junta de Andalucía, Grant PREDOC_00549.