Some locations contain rivers, artificial rivers, puddles and ponds. Decorative ponds are found in Honcho Shimoyashiki and Negishi Pavillion. Rivers are found in Sengen Town, Rokudo Valley, and Ryonin Market. Puddles are found in Phantom Forest and one of the corners of Ryonin Market.

They are all functionally the same. Running over a water surface will cause noise that will attract the attention of enemies, same as dropping heavy objects or corpses into it. Stealth killing an enemy over a water surface will make the ninja try to drown them into it, taking considerably longer than most stealth kills, surprinsingly the noise itself will not attract enemy attention.