Daniel Waterhouse is a fictional character from Neal Stephenson's The Baroque Cycle, a series of novels: Quicksilver, The Confusion and The System of the World .

Waterhouse is born in England in the mid 17th century to Drake Waterhouse , a prosperous Puritan merchant. Daniel is raised to be a minister, but instead is drawn to natural philosophy (i.e., science), which is just then emerging as an organized discipline. By virtue of becoming a college roommate of Isaac Newton, Waterhouse finds himself in the center of this important historical trend.

Later in life, Waterhouse leaves England for Massachusetts, in order to escape the feuds that are raging within the scientific community. He establishes the pathetic "Massachusetts Bay Colony Institute of the Technologickal Arts", which fails to attract a single student. He is rescued from this in 1713 by Enoch Root, who sends him on a mission back to England to forge a truce between Isaac Newton and his rivals (mainly Gottfried Leibniz), so that science can advance without needless distraction.

Daniel is an ancestor of Lawrence and Randy Waterhouse, characters from the novel Cryptonomicon.