Users of the Boundary Waters Canoe Area (BWCA) will swarm an updated reservations system Wednesday that’s designed to bolster cyber security and improve communication between paddlers and the U.S. Forest Service.

The new sign-up program opens at 9 a.m. for more than 100,000 camping, fishing and hunting enthusiasts who visit the million-acre wilderness from May 1 through September 30. Groups and individuals who want permits for popular weekends and those who covet high-demand locations will want to sign up early. Entry points and times are subject to quota limitations to prevent overcrowding.

“The shutdown has not affected the reservation system at all,’’ said Kristina Reichenbach, a spokeswoman for the Superior National Forest.

She advises permit seekers to be ready with alternate dates or entry points in case their ideal location or time has been booked by someone else. There’s a total of 42,840 overnight paddling permits available over the course of the season.

Pete Marshall, communications director for the nonprofit Friends of the Boundary Waters Wilderness, said some changes to the permitting system make it easier for people to plan their trips. But there’s also resentment on the part of many outfitters and some local residents over the elimination of a lottery system that doled out scarce permits to motorized areas of the BWCA, Marshall said.

He attended a “listening session’’ in Grand Marais earlier this month where outfitters, resort owners, guides and local BWCA visitors complained that the new system will hurt their businesses and lessen their chances to use Fall Lake, Basswood Lake and other waters where regulations allow boats with small motors.

Under the old system, motor lottery applications could be made via computer without deadline pressure throughout a four-week period. The system allowed outfitters to make applications on behalf of confirmed clients — an option that brought in important business, said Kerry Davis, owner of White Iron Beach Resort in Ely.

Now, with everything on a first-come basis, people who live in canoe country will be at a disadvantage in nailing down reservations, he said. Those who have faster internet service will win the race.

“They’ve really made it unfair,’’ Davis said.

Marshall said the local disenchantment is palpable.

“We do hope the Forest Service stays in close contact with outfitters’’ and local residents, Marshall said. “Having that local base and local connection to the area … is really important.’’

Permits via lottery contributed to some cases of stockpiling reservations and was already phased out for most entry points. Reichenbach said the latest changes go along with upgrades at the www.recreation.gov website to enhance financial security and privacy for users. BWCA reservations also can be made by calling 877-444-6777.