The shutdown comes as the rain and runoff threatens to send the Merced River into a flood stage.
Officials want to get everyone out, just in case the water reaches the roadways and threatens park facilities.
Ranger Jamie Richards explains, "We might lose power, there could be impacts to our sewer system and we wouldn't be able to have active restrooms open at that time, we might have problems to our water system, so we might have to shut off water to lodging and buildings in our valley."
For many, the closure meant a spring break trip to Yosemite cut short.
"We came from Australia, we wanted to visit here, but it looks like we have to leave by five, maybe come back another day," said Chanak Wjendra.
But those we spoke with seemed to be willing to make the most of what time they had.
"We came up this morning, just planned to come up for the day, and it's been beautiful to see the park in clouds and in a different way," said Kate Klorer from Big Bear.
The National Park Service says the plan is to reopen the valley, as soon as the weather permits it.
"As soon as the storm passes we are going to get park crews out there, start assessing systems, our power system our sewage system, make sure things are operational we are going to reopen the valley as soon as we can," said Ranger Richards.
Visitor services and campgrounds will remain open in Wawona, Hodgen Meadow, Crane Flat, and El Portal. The Big Trees Lodge, the El Portal Market, and the El Portal gas station are anticipated to remain open during the storm.
But the Park Service warns that any roadways and park facilities may close at any time for visitor and employee safety.