It begins in the Central Oregon Coast Range on the eastern side of the border between the two counties but crosses immediately west into Lincoln County through which it flows generally south to meet the main stem near Hamar Lake, north of Nashville.
The Little Yaquina has one named tributary, Cedar Creek, which enters from the right.
[3] Hamar Lake, along the Little Yaquina, covers 4.3 acres (1.7 ha) and has a shoreline of about 0.4 miles (0.6 km).
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