After making a backup, open your mod in FNVEdit and check to see what the GECK changed in the CELL records.
The WastelandNV worldspace has the 'Water needs adjusting' flag set. This is for the split level of water either side of the dam.
The cell records have corresponding flag 'hand changed'. Make sure the flags and heights haven't been reset to defaults.
BTW, this is a guess too
Although I have seen the missing water issue before and traced it to those flags.
EDIT: This is the CELL record for 12,12 in FNVEdit (so you know where I'm talking about)
FalloutNV.esm \ Worldspace \ 000DA726
\ Block 0, 0 \ Sub-Block 1, 1 \ 000DDDF7