Researchers in the Department of Civil and Environmental Engineering at the Pennsylvania State University released their Glacier Bay project page, which an be found at
http://www.engr.psu.edu/ce
The modeling was done using ADCIRC.
The project page is a good source of information on the oceanographic processes operating in Glacier Bay. It also incorporates coastal freshwater discharges through use of continuously variable non-zero normal flux boundary conditions.
The project pages contain extensive documentation on how to use ADCIRC and associated pre- and post-processing tools. The modeling project was done with an eye towards open source methods.