The lagoon's history has been traced back for more than 7,000 years. Until the mid-1800's, when European settlers arrived in the area, the lagoon maintained a relatively steady and consistent tidal flow and size, and functioned effectively as an ecological asset. The result of settlement by European-Americans has been a constant degradation of the lagoon's vitality, diminishment of its size, and deterioration of its ecological functioning, all caused by constantly increasing sedimentation. If present trends continue without intervention, the lagoon will fill with sediment and lose its ecological habitat value in a relatively few years.

Our earliest geologic maps (1850's) show an island free Bolinas Lagoon, which was navigable to the far northern end by shallow-draft vessels. Today, the far northern end is not accessible by any watercraft, and the main body of the lagoon is navigable by canoes and kayaks only, and only during high tide. Shallow-draft boats with outboard motors can use narrow channels near the mouth at high tide also.

Between 1968 and 1988 the lagoon lost twenty-five percent of its tidal prism (water volume capacity, over one million cubic yards) from sedimentation. In the past 30 years, the "upland" areas (dry land) surrounding the lagoon have increased by 67%. During this same period, the sub-tidal areas (deep water) have decreased by 29% and the inter-tidal (mudflats) by 5%. The sub-tidal and inter-tidal areas are where the ecological values of the lagoon reside.

Activities causing the increase in sediment buildup include grazing, tree harvesting, farming, rerouting a stream, and creating a recreational "inner lagoon" by dredging and disposing the dredge "spoils" into Bolinas Lagoon. Since the lagoon's destruction is being caused, and accelerated, by human interventions, it is appropriate that the lagoon be restored and preserved by human intervention.

In 1996 the Congress directed the U.S. Army Corps of Engineers to undertake an evaluation of Bolinas Lagoon and determine if there was a federal interest in preserving the lagoon as a functioning tidal estuary. The Corps decided that there was a federal interest in preserving Bolinas Lagoon's habitat values, and in 1998, in a joint venture with Marin County, undertook a multi-year restoration project; the first such project in Corps history justified solely by the ecological values to be preserved and benefits to be derived.