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The Alta did travel in both parts of the bay. In the book Sail and Steam on the Northern Calif. Coast 1850-1900 there is more than one reference made about the Alta traveling as far as the Bendixen Shipyard in Fairhaven to attend ship launchings - ironically the same place it was built in 1878. The steamer was built for the Arcata transportation company.
The Humboldt Bay is off of Eureka and the Arcata Bay is off of Arcata. The ferry must have gone through both, right?
That area is more formally known as Arcata Bay. Redwood trees in the surrounding hills were logged and rivers and streams carried silt down to the bay. A hundred years ago the bay was a deep water port. Today it is a mud flat at low tide.
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