waterhouse was of the family of waterhouse of halifax and was a resident of westminster. he was steward of the lands of oliver cromwell from 1651 to 1658. in 1656, he was elected member of parliament for monmouthshire for the second protectorate parliament as a replacement for a member who chose another seat. in 1659 he was servant to richard cromwell. he was elected mp for monmouth boroughs for the third protectorate parliament in 1659.