In November of 1909, Chicago publisher W.D. Boyce while on a visit to London, encountered the Unknown Scout and subsequently learned about the Scouting movement. When he returned to the U.S. he organized and then incorporated the Boy Scouts of America on February 8, 1910.

Through out the year the organization grew, and in September, 1910 reached western New York when the Rochester YMCA formed the area's first troop - Troop 1. Not long after, more troops were organized, and in February,1912 the Rochester Scout Master's Association was formed for the purpose of sharing experiences among units.

The movement continued to grow and the following year the Rochester Council was granted a charter on February 13, 1913. For the next decade and a half, the Council expanded to include Monroe, Orleans and Wayne counties. In December of 1932 the Monroe-Orleans District split away to form the Monroe-Orleans Council, and was shortly renamed the Red Jacket Council.

A decade later, the Wayne County portion of the Rochester Council was transferred to the Finger Lakes Council. On April 20, 1943, the Orleans County portion of the Red Jacket Council was transferred to the Lewiston Trail Council, and the remaining Monroe County portion merged with the Rochester Council to form the Otetiana Council.

On June 15, 2009, the voting members of Finger Lakes Council and Otetiana Council voted to merge. On September 5, 2009, the new name, Seneca Waterways Council, was approved.

Seneca Waterways Council is poised to continue serving the youth of Ontario, Wayne, Seneca, Yates, and Monroe counties for many years to come.