MIKE 21 is described as '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'. There are nine alternatives to MIKE 21 for Windows, Linux and Wine. The best alternative is Storm Water Management Model, which is both free and Open Source. Other great apps like MIKE 21 are HEC-RAS (Free), GeoHECRAS (Paid), MIKE 11 (Paid) and Delft3D (Free, Open Source).
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.
GeoHECHMS greatly speeds up the creation, analysis, and review of stormwater models. It automates subbasin delineation, curve number (CN) computation using land use and soils maps, and lag time (time of concentration) computation.
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.