This happens up the coast of Florida too in the Standard Edition. Fly around Miami or Fort Lauderdale you will a lot of marinas under water.
Lucky for you I fixed it then 
From the river mouth til the river separates I have fixed so far.
Will add I don’t have the orbx London city pack so it may or may not work with it, will have to try it won’t break anything literally just remove my file from the community folder if it causes any issue’s.
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The Thames runs uphill in a spot or two as well. It’s fun to fly in the Cub, nice and slow, cruising the Thames. 
I saw similar things along the coast. I think it is a conflict with people wanting water masking / transparency for some items and AI trying to guess the right mask vs no mask aspect. Smaller items to be addressed over time.
Or you maybe this is an alpha version of MSFS 2035 - Global Warming Edition
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Thanks, I will try and see.