Look at the map's entry in scenes.txt. The number before terrain code is water level, try setting it to lower value (terrain code is the thing that looks something like this 0x000000023002a1ba0004210900003ca000006a8900007a7b).
In example below, I highlighted number which is water level with bold
("mp_bavarian_river",sf_generate,"none", "none", (0,0),(100,100),-100,"0x00000001300005000008621800007b270000060500000d0b",
[],[],"outer_terrain_plain"),