Before asking, I did some searching and right about when I was going to give up, the combination
scifi story california fault major earthquake "inland sea" yielded "The Great Nebraska Sea" (1963) by Allan Danzig among its results, which was what I was looking for (ISFDb, Wikipedia).
It is available in The Internet Archive's copy of the August 1963 issue of Galaxy and on Project Gutenberg.
The story I've read, most likely in '90s or the late '80s, [...]
Very well possible; I most likely read it in 9th Annual Edition: The Year's Best S-F, edited by Judith Merril, which is among the books I got from my grandfather.
[...] portrays a bit of history how the USA got an inland sea. A previously ignored, presumably minor, fault line turns out to be bigger than previously thought.
The story opens with the fault.
Everyone—all the geologists, at any rate—had known about the Kiowa Fault for years. That was before there was anything very interesting to know about it. The first survey of Colorado traced its course north and south in the narrow valley of Kiowa Creek about twenty miles east of Denver; it extended south to the Arkansas River. And that was about all even the professionals were interested in knowing. There was never so much as a landslide to bring the Fault to the attention of the general public.
It indeed turns out to be a bit bigger.
By the mid sixties it was definitely established that the three Faults were in fact a single line of fissure in the essential rock, stretching almost from the Canadian border well south of the New Mexico-Texas line.
A series of earthquakes follow and a large part of the central USA sinks below sea level, creating an inland sea.
In the summer of 1973, the earthquakes start.
As the tremors grew bigger, along with the affected area, as several towns including Edison were shaken to pieces by incredible earthquakes [...]
They become more and more violent, until the Gulf coast drops and the sea rushes in.
The downtown section of North Platte, Nebraska, dropped eight feet, just like that, on the afternoon of 4 October.
From the north shore of Lake Ponchartrain to the Appalachicola River in Florida, the Gulf coast simply disappeared. [...] An hour later a wall of water had swept over every town from Dothan, Alabama, to Bogalusa on the Louisiana-Mississippi border.
And creates an inland sea.
Memphis was by now a seaport. The Ozarks, islands in a mad sea, formed precarious havens for half-drowned humanity. Waves bit off a corner of Missouri, flung themselves on Wichita.
The point of view in the story is looking back, telling the story of how the inland sea came to be, with dramatic losses, but that overall it turned out to be a boon for commerce and tourism.
Looking back from the (still) future.
Today, nearly one hundred years after the unprecedented—and happily unrepeated—disaster, [...]
Dramatic losses indeed.
But when the waters came to rest along what is roughly the present shoreline of our inland sea, it was estimated that over fourteen million people had lost their lives.
But beneficial to the economy.
[...] the commercial fisheries of Missouri and Wyoming contribute no small part to the nation's economy.
Who today could imagine the United States without the majestic sea-cliffs in stately parade from New Mexico to Montana?
Not even the tremendous price the country paid for its new sea—fourteen million dead, untold property destroyed—really offsets the asset we enjoy today. The heart of the continent, now open to the shipping of the world, was once dry and land-locked, cut off from the bustle of trade and the ferment of world culture.