Although released to minimal fanfare, The Book of Watermarks has retrospectively been assessed by critics as a unique and experimental entry in the catalog of PlayStation games.

[3] If the player is stuck, they are able to find and consult the titular Book of Watermarks to receive clues about where to go next, either identifying the location of the next puzzle, or providing a solution.

[8] Japanese magazine Dengeki PlayStation praised the "splendor" of the game's graphics, although found the movement of the camera slow and "unsuitable for impatient people".

[9] The Book of Watermarks has retrospectively been provided with more attention, with favorable reception of the game as a unique entry in the catalog of the PlayStation, and indicative of the appetite for Japanese developers to release unusual or experimental titles.

Simon Parkin of Eurogamer stated the game was "memorable" and part of an effort by developers "to paint their visions in full, often without compromise, in a way that only the best-funded independent game-makers are able to do today.

"[10] Similarly, in a retrospective of the PlayStation's twentieth anniversary, Edge cited The Book of Watermarks as an example of the "unusual curios" and "leftfield releases" on the platform.