When you say 'clearer' do you mean more transparent, or as is but less blue?
MGE replaces Morrowind's water with it's own if you have distantland enabled, and uses the non pixel shader water when distantland is disabled. There are replacement textures available for the non pixel shader water - try searching PES or TES Nexus.
MGE's water color and opacity is preset by the shader instructions thru InGame.fx and isn't easily changed, i.e. there is no user option thru MGEgui to adjust it. BTW, which version of MGE are you using? IMO the water looks most natural with phal's test/dev revision patch for d3d8 mge382 rev186 scatter+cloud v5 - see the end of the MGE FAQ for the link.
As this looks to be another MGE related question, please continue any posts in the MGE thread.