Because of the high deposition rate of the river, which threatened to ruin San Diego Bay as a harbor, the federal government diverted the flow into Mission Bay and built a levee embankment, Derby Dike, of earth extending from near Old Town to Point Loma in the fall of 1853 (Derby 1853).

Later that year, heavy rains caused the river to change course once again, washing out part of the levee and resuming its old course into the harbor (San Diego Herald 1855).

This was part of the Great Flood of 1862, which impacted the entire Western United States, and had a bearing on the Civil War.

In San Diego, Mission Valley was inundated, and houses in lower Old Town were flooded when severe winds from a sea storm from the south backed the water up from the bay into the river (Pourade 1964:250).

Since then, a considerable volume of sediment has been added to the San Diego River delta in Mission Bay from occasional floods.

In 1935 El Capitan Dam was constructed 27 miles up the San Diego River; this reduced the sediment entering the bay considerably.

The flooding became so extreme that land owners on either side of the San Diego River got together to hatch a plan to contain the 100 year/1 hour rain events.

Two men, Dean Wolf (of Mission Valley Center) and Denny Martini of the Bond Ranch (who owned ¾ of Mission Valley in 1908); conceived the idea of straightening out the San Diego River to prevent "back flow" along the natural curves where flooding took place.

10 years and over a million dollars was spent developing a plan to build a series of box culverts with rip rap, “hump back” river banks, islands, and hydro seeding.

Additionally, land would be donated to the City of San Diego for the construction of the Trolly to help alleviate traffic congestion.

One important goal is to help create a river-long park and hiking trail, stretching the full length of the river from its headwaters in the Cuyamaca Mountains to the Pacific Ocean.