GOTM - www.gotm.net

GOTM (General Ocean Turbulence Model) is an ambitious name for a one-dimensional water column model for marine and limnological applications. It is coupled to a choice of traditional as well as state-of-the-art parameterisations for vertical turbulent mixing (see gotm.net).

GETM - www.getm.eu

GETM is a 3D numerical model simulating the most important hydrodynamic and thermodynamic processes in natural waters. The model is general in the sense that it can be applied to various systems, scales and specifications (see Bolding-Burchard.com).

others: 

Two layer model - originally developed for simulating Baltic Sea inflow events - was written during a master thesis (03/2006) at the Baltic Sea Research Institute of Warnemünde.

A list of useful scripts for the use of these models can be found here. Some idealised and realsitic model setups can be found here.