Quickest 6h 15min
There are 1 ferry company operating from Seldovia Harbor to Juneau Harbor, 4 flights from Seldovia Harbor to Juneau Harbor. The cheapest ferry costs $380 and is 2d 40min.
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There are 2 ways to travel from Seldovia Harbor to Juneau Harbor. 4 ferries and 4 flights are possible between the two areas. The flight from ENA to JNU is the cheapest and fastest. The ferry operated by Alaska Marine Highway System running from Seldovia Harbor to Juneau Harbor is the most convenient.
It's important to check each mode when booking your ticket so that you can find the best method for you. The cost of each type varies differently, so be sure to use Faretrotter to keep an eye out!