The lagoon water level is regulated on a seasonal basis to optimize flood control, recreation, aesthetics, and ecological benefits. During the winter the water level is lowered to provide a receiving basin for stormwater runoff as protection from lowland flooding. The summer water level provides optimal conditions for swimming, boating, and other recreational uses. The water level is controlled using the O’Neill Slough intake gates on the lagoon's south end and the Marina Lagoon Pump Station on the north end. The Pump Station's pumping capability, in combination with the winter operating level of 94.9 feet, provides the capacity for a 100-year storm event.

Marina Lagoon Operating Levels

Period	Level Adjustment	Elevation (ft)*	Comments
May 1 – October 31	-----	96.9	Summer operating level
November 1- November 30	-1 ft.	95.9	Preparing for winter rains
December 1 - January 14	-1 ft.	94.9	Winter operating level
January 15 - February 15	-1.5 ft.	93.4	Dock maintenance period
February 16 - March 31	+1.5 ft.	94.9	Winter operating level
April 1 - April 30	+ 1 ft.	95.9	Spring intermediate level
May 1 - October 31	+ 1 ft.	96.9	Summer operating level

*Elevation reference is the San Mateo datum +100.