Assuming you're using at least MGE v3.8.2 rev-0178, you can adjust the depthcolor which influences the surface color of MGE's water.
Find the following line in InGame.fx:
static const float3 _depthcolor = _lightfactor * SunCol * float3 (0.03, 0.04, 0.05) + (SkyCol + 0.5*FogCol2) * float3 (0.075, 0.08, 0.085);
The two 3-number sets are RGB values - adjusting them will change the color of the water as viewed from above surface.
Try these settings:
static const float3 _depthcolor = _lightfactor * SunCol * float3 (0.03, 0.075, 0.125) + (SkyCol + 0.5*FogCol2) * float3 (0.075, 0.125, 0.2);
Since that only affects the surface color, you'll probably also want to change your Morrowind.ini settings for [Water] section >> UnderwaterColor ; adjusting UnderwaterColorWeight might be warranted as well.
[edit] note that the changes to _depthcolor only affect exterior water. Interior water does not have Sun color or Sky color, which is what those RGB values are associated with and influencing.
[edit2] you might like these values better:
static const float3 _depthcolor = _lightfactor * SunCol * float3 (0.03, 0.06, 0.10) + (SkyCol + 0.5*FogCol2) * float3 (0.075, 0.12, 0.17);
Coupled with these values for Morrowind.ini under water color & weight:
UnderwaterColor=012,045,074
UnderwaterColorWeight=0.875