Hello
We have too few informations about your model (mesh, boundaries, tide effects, wetting and drying, calibration, etc...). We can not give straightforward instructions.
The variations of free surface and velocities are extremeley low. You are, thus, deeply in the margin of uncertainties (of measures, calibrations (choice of friction coefficients), input data, mesh discretization etc.). That's why, in my opinion, the random variation of the head can not be exploited significantly.
A last recommendation, use the double precision format for your geometry file and particularly for your result file, this could help to minimize trancation errors. (use RESULT FILE FORMAT = 'serafind', GEOMETRY FILE FORMAT='serafind' (need to be generated in double precision with mesh generator, otherwise useless)).
I hopte that this helps
with my best regards
Riadh