Idea by @Thomas V. Meyer

The most effective method to prevent flooding of properties adjacent to the Canal (San Rafael Creek) is to install a flood gate system similar to the one installed in Venice, Italy to prevent the repeated flooding of that city. Whenever king tides (or tsunamis) are expected, these gates can be closed to prevent water from San Francisco Bay/San Rafael Bay from entering the Canal. This one mechanism would protect every parcel of land along the canal as well as prevent flooding of the streets in the Canal neighborhood. It would likely be a costly undertaking but that fact that a flood gate would eliminate the need for all the homes and businesses along the Canal as well as the City of San Rafael, to install their own flood barriers which would likely entail a greater total cost, assuming that all residents and businesses would undertake such preventative measures. The Italians have already done all the engineering and design, so that expense is taken care of.