In reply to Geoboy:
It's been a while since I did finite difference methods, but from memory each method (implicit, explicit, crank-nicholson etc.) each have different properties that make them more or less suited for certain applications.
From the FDM wikipedia article:
"Usually the Crank–Nicolson scheme is the most accurate scheme for small time steps. The explicit scheme is the least accurate and can be unstable, but is also the easiest to implement and the least numerically intensive. The implicit scheme works the best for large time steps."
As you said stability can also be an issue so that will have been taken in to account when choosing the scheme.
The wikipedia article also has a little more detail about the advantages/disadvantages of each, the bit on errors may be particularly helpful:
https://en.wikipedia.org/wiki/Finite_difference_methods#Example:_The_heat_e...
Im in no way familiar with sediment transport, but presumably you're looking at fairly large time intervals which would make the implicit method a good choice as it's relatively accurate with long time steps (i.e. less computation needed to run the model for long time periods.)
Other than that finite difference methods are just a way of solving differential equations. The real magic will be in how the differential equation itself is put together, what assumptions are made, why those assumptions are reasonable etc. That'll be where all the parameters will come in to play (although they may then appear when you're solving with the FDM). Having said that there will be a certain amount of tuning step sizes to get the required accuracy while not having a crazy computation time.
You can think of implicit FDM as an algorithm for approximating the solution to differential equations. That is the precise implementation might vary a little but the answer should always be pretty similar (disregarding issues like the numerical precision of the variables used in the program of choice.)