Yes. On a large development project such as building a new house, the City may ask you to submit a drainage plan, prepared by a California licensed engineer, as part of your application to develop your property. The installation of drainage facilities on such a project would be inspected by the City for compliance with the property owner's plan. Tie-ins to public drains or gutters in the public right-of-way require an Encroachment Permit.
Large-scale projects, such as rerouting the course of a storm drain or channel, require a Watercourse Modification Permit issued by the Department of Public Works. Work within a creek requires review and approval from several regulatory agencies, including the Regional Water Quality Control Board, the Department of Fish and Game, and possibly the Army Corps of Engineers. For further information, see the Department of Public Works fact sheet regarding work near creeks.