This is a subject near and dear to me because I live next to the Chesapeake Bay, a body of water continuously influenced by "civilization" since the 1600s.
Probably the best source of what underwater visibility was like 400 years ago was the Journal of Captain John Smith (the same guy that married Pocahontas). He described an area I'm very familiar with - Lynnhaven Inlet and the Broad Bay - as so clear that you could see all the way to the 30 FT bottom. He saw so many blue crabs in the sand that if they swam to the surface he could have walked across the water on their backs.
Another "old" source, a guy called Count Zinzindorf who was a traveling companion of explorer and botanist William Bartram in 1742 along the North Branch Susquehanna's thickly forested shores, described "beautifully transparent" water, so clear that swimming chin deep, they "might have seen a pin at the bottom."
If you went to either of these places now and were lucky to dive them on a GOOD day, you might get to see your hand in front of your face.
As for all of our "accomplishments" at improving water quality in the Chesapeake Bay during the last 30 years, just watch the "making of the Chesapeake Bay Bridge Tunnel (CBBT)," a "Modern Marvels" episode on the History Channel when it airs again. They show CBBT construction films that had BLUE WATER in the Chesapeake Bay during 1963!
As late as the 1980s, I dived the islands of the CBBT and had 40+ FT of underwater visibility routinely. Dive shop boats did openwater certification trips to the islands regularly during the summer and "after work" night dives on Wednesdays and Fridays. Now? No one runs to the islands anymore because visibility on a good day might be 10 FT, usually less.
So what's the problem? Simple answer, land runoff. All the crap draining from parking lots, streets, sewers, factories and other stuff, just when it rains, puts sediments into the water. I shudder to think about all the salt and other chemicals that went into east coast rivers during the snow storms of last winter.
It's not good...