A small, salt-water pest could cause a big crisis for Big Apple lox-aholics.

The half-inch-long sea louse — Lepeophtheirus salmonis — is killing off huge numbers of juvenile wild salmon in Europe and Canada, which means the price of the city’s favorite brunch treat could jump higher than a spawning sockeye.

The parasite, which clearly enjoys dining on the fish as much as New Yorkers do, caused global salmon supplies to dip by 9 percent last year.

Meanwhile, algae blooms last year at Chilean fish farms caused yet another juvenile salmon die-off, which experts say will drop supply still further this winter.

As a result, wholesale prices have climbed by 40 percent to 50 percent in recent months, according to experts in the United States and Britain, the Guardian reported last week.

“They’re only a couple of inches long, and the lice basically eat them alive,” British Columbia, Canada-based marine biologist Alexandra Morton told The Post on Saturday of the juvenile wild salmon that are catching lice from farmed fish throughout eastern Canada, Norway, Scotland and Ireland.

The wild and farmed salmon come into contact because the farmers build their fisheries along rivers to save money, she said.

“The worst case scenario? Extinction of wild fish in the areas where there are these farms,” she said.

For now, wholesalers and resellers are absorbing much of the cost increase.

“It’s gone up 50 cents to a dollar a pound just in the past couple weeks,” griped Lewis Spada, co-owner of Shelsky’s Appetizing and Delicatessen in Cobble Hill, Brooklyn, describing his spiraling wholesale costs to The Post on Saturday.

But uncertainty abounds. Will lox stocks barrel downward? Will delis start scaling back?

“It’s delicious, but 50 percent more — holy smokes!” Nova-lover Chris Hartland, 28, told The Post while noshing at Russ & Daughters on Houston Street.

“We paid $30 for two bagels [with lox and cream cheese], and we’re still hungry!”

“Oh man, my daughter would die without her lox and cream cheese on a bagel most mornings,” Jonathan Walsh, 40, of the Upper East Side, said at Zabar’s Eli’s Market.

But the country’s biggest supplier of smoked fish, Greenpoint-based Acme Smoked Fish, said dire predictions of a lox lockout are just a schmear campaign.

“There will still be as much lox as people want,” insisted David Caslow, co-CEO of Acme.

“My personal expectation is we are somewhere in the peak of losses and high prices now.”

Acme — which supplies Shelsky’s and other iconic emporiums, including Russ & Daughters, Zabar’s, Kossar’s and Barney Greengrass — has a major plant in Chile that “puts us in a very adventageous mode with Chilean farms,” said the company’s sales head, Buzz Billik.

“No one else in the US is in a better position to satisfy the market,” according to Billik.