The sudden importance of the region increased the urgency of fixing an exact boundary. There were reports that Canadian citizens were harassed by the U.S. as a deterrent to making any land claims. In 1898 the national governments agreed on a compromise, but the government of British Columbia rejected it. U.S. President McKinley proposed a permanent lease of a port near Haines, but Canada rejected that compromise.The economy continued to grow and diversify. Four canneries were constructed around the mission by 1900. However, the completion of the White Pass and Yukon Route railway in neighboring Skagway that same year led to the Dalton Trail's eventual abandonment and Haines' economic decline.

Haines is much more accessible than most other southeast Alaskan communities of its size, as it is connected to the North American highway system by the Haines Highway, which passes through British Columbia on its way to the junction with the Alaska Haines can be reached via the 159-mile Haines Highway which branches from  the Alaska Highway 100 miles north of Whitehorse at Haines Junction. The Haines  highway was built in 1943 and is now one of Alaska's best and most scenic  highways. The town is served by the Alaska Marine Highway System, as well  as scheduled air and bus transportation.