Looks like you misremembered or misread the map? "Lake Lahontan was a large endorheic Pleistocene lake of modern northwestern Nevada that extended into northeastern California and southern Oregon." It was mostly in what's now Nevada, and there's a clearer map here: https://en.wikipedia.org/wiki/Lake_Bonneville#/media/File:La...
you don't have to go that far back. A little more than a century ago the California central valley looked very different. Tulare Lake was the largest fresh water lake west of the great lakes, bigger than Tahoe[1]. Of course there's also Hetch Hetchy, which supplies San Francisco's water[2]. Countless other engineering projects have vastly changed the flow of water in the state.
It's always seemed so bonkers to me that Yosemite National Park was made in 1890 and yet Hetch Hetchy, which was part of the park, was dammed in the early 1920s. I get that it was a different time and all, but come on, you can't go around destroying part of a NP like that.