Sorry, didn’t look at this forum for some days. This is the water-shader.
// after siwa_water2:
textures/river2nd_t/rv2nd_water // surface of water - no proper fogclipping
{
// nocompress // no idea why this is here
qer_editorimage textures/river2nd_t/rv2nd_water.tga
qer_trans 0.5
qer_nocarve
q3map_globaltexture
// surfaceparm nomarks
surfaceparm nonsolid
// surfaceparm trans //disabled to make surface opaque
surfaceparm water
// surfaceparm fog // fog inside the watershader
// fogparms ( 0.08 0.18 0.17 ) 2048 // disabled cuz doesnt work
cull none
nopicmip
deformVertexes wave 64 sin .25 .25 0 .5
nofog //disable to have the water clipped by fog but it makes the surface transparent then and u get worldspawn fog in the water
// waterfogvars ( 0.08 0.18 0.17 ) 0.2 // ( 0.11 0.13 0.15 ) 0.2
{
fog on
map textures/river2nd_t/rv2nd_water.tga
blendFunc blend
alphaFunc GE128
rgbgen identity
tcmod scale 1 1 //0.5 0.5
tcmod scroll -0.2 -0.1//-.02 -.001
}
{
fog on
map textures/liquids_sd/seawall_ripple1.tga
blendFunc GL_ONE GL_ONE
rgbGen wave sin 0.3 0.02 0 0.25
tcmod scale 0.01 0.01 // me: 0.04 0.05
tcmod scroll .0025 -.0015 // -.001 -.0002
}
{
fog on
map textures/liquids_sd/seawall_ripple1.tga
blendFunc GL_ONE GL_ONE
rgbGen wave sin 0.1 0.03 0 0.4
tcmod scale 1 1
tcmod scroll .009 -.006 //old:.005 .003
}
{
fog on
map textures/liquids_sd/siwa_shimshim1.tga
blendFunc GL_ONE GL_ONE
rgbGen wave sin 0.4 0.02 0 0.3
tcmod transform 0 1.5 1 1.5 2 1
tcmod scroll .01 .01 //.005 -.001
}
}
From what I found out it seems to be the blendings… the Battery ocean1 works fine with fog, but I wasn’t able to make it non-transparent. The ocean0 clips even better, but using my textures in it makes it look as if the different blends are (z-)fighthing each other then. However I need opaque water for the gameplay.
My derivate of the ocean1 shader:
textures/river2nd_t/rv2nd_water1
{
q3map_baseshader textures/river2nd_t/river_base
cull none
deformVertexes wave 1317 sin 0 2.5 0 0.15
deformVertexes wave 317 sin 0 1.5 0 0.30
// {
// map textures/liquids_sd/seawall_specular.tga //disabled this assuming its for the sun-on-water-effect, but it made no significant difference to my prob
// blendFunc GL_ONE GL_ONE
// rgbGen vertex
// tcGen environment
// depthWrite
// }
{
map textures/river2nd_t/rv2nd_water_02_d03.tga
blendFunc blend
rgbGen identity
// alphaGen const .8
tcmod scale 1 1 //0.5 0.5 //from siwa
tcmod scroll -0.2 -0.1 //-.02 -.001 battery: 0.005 0.03
}
{
map textures/liquids_sd/seawall_ripple1.tga
blendFunc GL_SRC_ALPHA GL_ONE
rgbGen wave sin 0.2 0.1 0 0.2
alphaGen vertex
tcMod turb 0 0.05 0 0.15
tcmod scale 0.01 0.01 // me: 0.04 0.05
tcmod scroll .0025 -.0015 // -.001 -.0002
}
{
map textures/liquids_sd/seawall_ripple1.tga
blendFunc GL_SRC_ALPHA GL_ONE
rgbGen wave sin 0.15 0.1 0.1 0.15
alphaGen vertex
tcMod turb 0 0.05 0.5 0.15
tcmod scale 1 1 //0.5 0.5 //from siwa
tcmod scroll .009 -.006 //old:.005 .003
}
}
Should I say that I have no clue here what I m doing? lol… this is real trial and error when I mess with the shaders 
This is the original thread on this prob in the ET forum where I posted a lot more details on what I tried so far:
http://www.splashdamage.com/index.php?name=pnPHPbb2&file=viewtopic&t=10247
This is another thread on bad clipping and fog, this time for sky-fog and terrain:
http://www.splashdamage.com/index.php?name=pnPHPbb2&file=viewtopic&t=10396