Yaquina Bay is named after the Yaquina Tribe that occupied the territory along the Yaquina River. With the railroad addition In the late 1880s, many thought Yaquina Bay would be the commerce center for the Pacific Northwest. Wheat, lumber, and other goods were transported to Yaquina Bay as the area began to develop. Oyster companies and other merchandise organizations began to take residence in the Bay.
American Indians had called Yaquina Bay home for years until the westward expansion. In 1856, the first vessel entered Yaquina Bay carrying supplies for Siletz Block-houses up the Yaquina River. The newfound Bay access promised a great deal of advantages, particularly open transportation and shipping to and from San Francisco Bay. Also in 1856, a doctor from the Willamette Valley was appointed surgeon to an Indian agency in Yaquina Bay. Following Indian trails through the Coast Range, the doctor, along with three other explorers, set out for the coast in quest for his new appointment.
In 1861, Captain Spencer, from the state of Washington, first settled in Yaquina Bay. Spencer, with the assistance of a local Indian guide, discovered valuable oyster beds within the Bay, which would attract future businesses, particularly firms from San Francisco.
In 1866, news spread of the promises and new life Yaquina Bay had to offer and quickly brought a surge of settlers to the area. Newport was quickly formed and oyster companies and other industries began to take resident. The growing oyster business initiated the construction of a wagon road from Corvallis to Yaquina Bay, costing approximately $20,000 and spanning 45 miles. The road was completed in 1873 and promised continued connections between Corvallis and the coast, and even helped settlers reach their new coastal home.
With the influx of residents, seasonal visitors to the area, and booming businesses, Yaquina Bay’s oyster trade quickly began to decline. In 1869, a group of oystermen formed a task force with the interest of preserving oyster beds. To better the public's interest and their own, they worked diligently to restore and protect the oyster communities.
Shortly after the establishment of Newport, the Yaquina Bay lighthouse began construction in 1871. However, with the establishment of the Yaquina Head lighthouse to the north, it was decommissioned in 1874.
For a long time, Yaquina Bay was the midpoint between San Francisco and Seattle. With increased ship and navigation traffic into the area, the number of shipwrecks increased rapidly.