Juliane,
A few ways to do this:
One way to do this is if you have a polygon feature class for water, set this as a Mask in the Raster Analysis Environment Settings. From there, open the Raster Calculator and set the map algebra statement to be bathymetry raster as the only input and define the output raster. The mask will "clip" the raster for those areas that the water and bathymetry raster intersect.
Another way is to use the Extract by Mask geoprocessing tool - even easier! Define the bathymetry as the input raster, the water as the mask, and define the output raster.
Good luck!
Robert LeClair
Esri-Denver