Over the years, the Pajaro River has had a long and storied history of flooding and flood control projects. Since 1966, the Corps has conducted planning with the City of Watsonville and the Counties of Monterey and Santa Cruz in an effort to provide the communities along the river with adequate flood protection. In the past 40 years, over 23 flood protection alternatives have been explored to control waters of the mainstem Pajaro River from the ocean to Murphy Crossing Road and along Salsipuedes and Corralitos Creeks, which drain into the Pajaro in the City of Watsonville.
The 19 alternatives considered over the years fall into six main categories:
| 1936: | Federal Flood Control Act authorizes flood control |
| 1949: |
Levee system construction is completed along the Pajaro River and Salsipuedes Creek |
| 1955: | First major flood event to breach levees |
| 1966: | Federal Flood Control Act authorizes new project |
| 1974-75: |
Local community declines to support any identified project alternative |
| 1982-86: | Flooding occurs along the Salispuedes and Corralitos Creeks |
| 1995: |
Major flood event breaches Pajaro River levees; flooding occurs at less than the design capacity |
| 1997: | Flooding occurs along Corralitos Creek |
| 1999: |
Pajaro River mainstem is combined with Salsipuedes/Corralitos Creek project under federal authorization |