Clouds in composite1.fsh
Water in gbufferwater.fsh
1 Search for CloudColor2 (if you want to change the speed of volumetric clouds) or CloudColor (2d clouds)
2 Search for ", courier, monospace">float t = frameTimeCounter * [speed];
3 You can just lower the speed number.
1 Search for GetWaves
2 Look at ", courier, monospace">float speed = 0.9f;
3 Change the 0.9f to something lower.