SOBEK Suite is described as 'SOBEK is a powerful modelling suite for flood forecasting, optimisation of drainage systems, control of irrigation systems, sewer overflow design, river morphology, salt intrusion and surface water quality'. There are eight alternatives to SOBEK Suite for Windows, Linux and Wine. The best alternative is HEC-RAS, which is free. Other great apps like SOBEK Suite are Storm Water Management Model (Free, Open Source), MIKE 11 (Paid), Delft3D (Free, Open Source) and GeoHECRAS (Paid).
GeoHECRAS speeds up HEC-RAS model creation using AutoCAD and GIS data sources. Work directly off of Google Maps, viewing and editing the model in 2D and 3D. Automated cross section cutting reduces time in building a model.
MIKE 21 is the ultimate Swiss army knife of coastal modelling. If you need to simulate physical, chemical or biological processes in coastal or marine areas, MIKE 21 almost certainly has the tool you need.