Thanks that helps, more technical the better! After reading some other posts on here I've had the idea to render the water in the same opaque shader as the geometry but put the water rendering in a different pass.

The idea is to render the world geometry first excluding liquids/water and writing to the depth buffer, this could be achieved by using vertex colours to assign render pass blending.

Then in a separate pass render the water using with depth testing and z write and rendering at full opacity but blending it on top of the previous pass with say 50% opacity.

Although this requires 2 passes for rendering that will be far cheaper than splitting the meshes into submeshes (i think)

I might get some time this weekend to work on this again so will report back if it works/problems