With the caveat that I'm only just getting started trying to model an IRL location, could be completely wrong, and your life may be in danger if you follow anything I say...
I don't think the custom water map works quite like that. In my testing (attempting to put water into heightmapped IRL riverbeds and lakebeds, including mountain streams), the custom water map appears to
override the global map water level. That is, if you add a custom water map into the mix, the 43 level that you entered is simply ignored. The only places water will show up on your map are places which have non RGB(0,0,0) grey colors.
And but so, if you want your riverbeds to be dry,
but also to have water elsewhere on the map, you have a couple of options I think (please read the caveat above again, and put on a helmet before proceeding):
1) Make sure your dry riverbeds are higher in elevation than places where you want water, then just use the global water level (43 perhaps) to fill in the lower-lying water areas and the higher-elevation dry beds will remain dry.
2) Create a custom water map which paints out
all of the water you want. Every non-dry lake and river must be painted in non-(0,0,0) colors appropriate for the local elevation. For example in my own world I might have a mountain lakebed at elevation 180, and the rim of the lake is elevation 190. If I paint that area (does not need to be precise - just cover the surface area of the lake) with (188,188,188), then water level in that area will be 188, filling the lake to within 2m of the rim.
My map has a few large rivers and a couple of lakes. I'm having to hand-paint all of them since they are all at different elevations. Hope that helps. Assuming I'm not 100% wrong!
Edit to add: below is my work-in-progress water map (on a white background; the white would not be exported to png). It all looks black here, but actually it is copied out of the original heightmap of the IRL location. If I were to try to use this, the water levels would be precisely at surface-level in the areas shown. The work-in-progress is me "sinking" the heightmap in just these areas by a couple/few meters, then sinking the watermap by 1m to put the water just below the rim of the river/lake.
The overall point is that water will
only show up in these areas. No matter what I put into the KG global water level. At least that's been my experience in testing so far.
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