Northbound traffic and half the pedestrian crossings at the San Ysidro border point were shut to install new movable wire-topped barriers.
Around 110,000 people enter the US daily through the crossing.
In the Mexican border city of Tijuana residents held protests demanding the migrants leave the area,
Mayor Juan Manuel Gastelum said on Friday he expected the number of migrants arriving in the city in the coming weeks to reach 10,000, warning the city was not prepared to handle the "avalanche".
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