Does anyone have experience creating water waves? I want to look at waves striking a dock piling.

I started by writing a function to vary the water height at my inlet using a simple sine function, the wave doesn't propogate downstream however, instead it reverses back on itself and after awhile disappears

You need to specify more than a displacement as an initial condition for travelling waves. A left moving wave and right moving wave may well have the same shape (displacement) at an instant in time but they will have different particle velocities.By (presumably) specifying a zero particle velocity you have not specified any overall movement of mechanical energy in one direction or the other (think force*velocity). Often this will give you equal right and left moving waves (i.e. drop pebble in water) but if you are doing this at the boundary then your boundary conditions may well interfere.