The boot well is about 2cm deep with water. All around the battery, and around the fuse boxes. 

I've been in the boot, with it closed,  while someone poured water over it. But saw nothing coming in.

Taken the lights out, no obvious signs there. 

Had a good look all around, just can't see how it's getting in! 

Any ideas please? 

You are not alone. Search forum topics for "water in boot" to see other instances of this problem and how many people have tried to cure it, often unsuccessfully.

Could be a failing boot seal. 

Water will find the path of least resistance to get in. Obvious suspects are rubber boot seal, rear lights and equalising vents behind the rear bumper. In extreme examples, even down to bodywork seam sealer or lack of it! If it’s avant, there’s the possibility if rear wash wipe. Units are made by Valeo and copper/brass pipe is known weak point to shear.

To show the extremes you may need to go to, watch this. 

Moving forward, strip out the boot trim or tailgate trim, so you are down to bare metal. Line the boot area with paper towels, held in place with masking tape. Shouldn’t take long to identify source, which you can then get visual on.