About two dozen people were taking part in the demonstration Monday morning when deputies arrived. Most agreed to leave, but three remained locked to each other on the tracks.
The sheriff's office says they ultimately unlocked themselves and were arrested for criminal trespass.
Emily Johnston, a spokeswoman for the protesters, identified the three as 62-year-old Annette Klapstein, a retired lawyer from Bainbridge Island; 28-year-old Adam Gaya, of Seattle; and 60-year-old Jan Woodruff, of Anacortes.
Johnston says the derailment last Thursday in Seattle of a train carrying volatile Bakken oil from North Dakota to the refinery highlighted the dangers of shipping the oil by rail, and they want all shipment of the oil through Northwest communities brought to an immediate halt.
No oil was spilled in the Seattle derailment.