"this is so deeply embedded[ stuck into] in the water supply" Maybe it refers to pollution in the water.Or there could be something else that is in the water supply.

a set of societal constructs so deeply embedded in the water supply that we take them for granted.....

It means exactly what it says. Which part don't you understand? You can look up the word "embed".

Water supply -The source of water provision. Where the water inquestion comes from.

"water supply" is it concerns human?