Did this one accidentally did.
Using the Timepiece go back in time and take out the 2 guards. Once they are gone grab the wheel inside of the case in the back corner of the room and take it through the hole in the wall. Attach the wheel to the spot on the wall. Go back into the present and hop in the water and turn the wheel. The water will subside and the crate will sink to the floor where you can then grab the rune and pop - Flooded Basement Trophy.
P.S. I've read this Trophy can be buggy and apparently reading the note outside on the wall can cause the Trophy to pop after you've done everything else.