Streams and sloughs that enter into Humboldt Bay are listed north to south, clockwise, with tributaries entering nearest the bay listed first.
The primary streams of major watershed areas east of the bay (draining a combined area of 288 square miles (746 km²)) are in bold.

Mad River Slough
Liscom Slough
Janes Creek (enters the bay as McDaniels Slough)
Jolly Giant Creek (enters the bay as Butcher Slough)
Campbell Creek (partially channeled to Gannon Slough)
Fickle Hill Creek
Gannon Slough
Grotzman Creek
Beith Creek
Little Jacoby Creek
Jacoby Creek
Washington Gulch Creek
Rocky Gulch Creek
Eureka Slough
Fay Slough
Cochran Creek
Freshwater Creek
Little Freshwater Creek
Ryan Slough
Ryan Creek
First Slough
Second Slough
Third Slough
Clarke Slough
Elk River
Swain Slough
Martin Slough
Willow Brook/White Slough
Salmon Creek
Deering Creek
Little Salmon Creek
Hookton Slough
Streams and sloughs that enter into Humboldt Bay are listed north to south, clockwise, with tributaries entering nearest the bay listed first. The primary streams of major watershed areas east of the bay (draining a combined area of 288 square miles (746 km²)) are in bold.
Mad River Slough
Liscom Slough
Janes Creek (enters the bay as McDaniels Slough)
Jolly Giant Creek (enters the bay as Butcher Slough)
Campbell Creek (partially channeled to Gannon Slough)
Fickle Hill Creek
Gannon Slough
Grotzman Creek
Beith Creek
Little Jacoby Creek
Jacoby Creek
Washington Gulch Creek
Rocky Gulch Creek
Eureka Slough
Fay Slough
Cochran Creek
Freshwater Creek
Little Freshwater Creek
Ryan Slough
Ryan Creek
First Slough
Second Slough
Third Slough
Clarke Slough
Elk River
Swain Slough
Martin Slough
Willow Brook/White Slough
Salmon Creek
Deering Creek
Little Salmon Creek
Hookton Slough
Humboldt Bay