Returned from a two week cruise and the 2016 E350 had been parked outside. Usually the car is parked in a garage, so maybe that’s why it hasn’t happened before. Anyway, I opened up the trunk and there was about half an inch of water collected in the Weathertech liner I have in there. Once home, I removed that, and discovered there was water under the liner, indeed, all the way down in the spare tyre well, albeit much less.
It’s still in warranty, so I will let the dealer take a look. However, I couldn’t find any obvious problems with any of the usual suspects, eg boot lid seal, taillights, channels, etc.
Has anyone else experienced this?

Neighbor playing tricks with the hose? That’s a lot of water. Move north where the snow won’t cause this. Lol