Countless local residents and officials, including San Diego’s powerful Republican mayor, Kevin Faulconer, say the abrupt transfer of hundreds of officers from ports of entry has put the daily flow of bodies and goods through checkpoints in slow-motion, interrupting the region’s cross-border economy. Wait times frequently exceed four or six hours.

“Having our borders open and fully functioning is not an option, but a necessity,” Mayor Faulconer said in a statement, when asked about the extensive delays, which he tersely described as having a “negative impact.” The San Diego Association of Governments — a state regional agency — recently estimated that about $7.2 billion in gross output and more than 62,000 jobs are lost annually because of border traffic. And stoppages have only gotten worse this spring with the manpower shortage, which has led to commercial lane closures.

As President Trump renews threats to close the border outright, customs brokers tell me their partners — in cross-border supply chains for aerospace, medical devices and agriculture — are “panicked.” Eduardo Acosta, vice president of a major customs brokerage company, says businesses are facing late fees, contract cancellations and assembly line freezes.“All that adds up,” Mr. Acosta said. “Twenty percent of cargo being laid over every day.” Another executive, Fidel Gutierrez Castro, C.E.O. of G-Global, agreed: “They have us all crazy, making contingency plans.” Places like the El Paso-Ciudad Juárez area in Texas, while not as heavily transited as Southern California, are also reporting disruptions.

Ports of entry are at the center of hotly debated legal questions about asylum seekers — in the courts and in the media. Last month, nearly 11,000 asylum seekers legally entered the United States through them. About 53,000 families crossed illegally.

Those here on the ground know that part of the decade-high surge in illegal crossings is directly linked to the long backlogs at ports of entry. Many migrants who fear for their lives in Mexico, or who don’t want to wait, cross illegally to avoid delays at the ports. (For asylum seekers, the wait time is weeks.) And with White House rhetoric painting a bleak picture of a lawless border, more armed militia groups have been heading here to detain these families at gunpoint, long before contacting the Border Patrol.