Financial terms of the agreement were not immediately available.
CHS said the operations, which are in Alberta and Saskatchewan, will become part if its Country Operations division.
The locations will be able to take advantage of a new fertilizer plant outside Shelby, Mont., the company said.
The sale is expected to be completed on or about April 1.
In addition to its retail business in North America, South America and Australia, Agrium is also a wholesale producer and seller of crop nutrients and specialty fertilizers.
The sale of the 16 locations was part of a deal last year Agrium agreed to in order to win approval from the Competition Bureau for the company's acquisition of a large chunk of Viterra's retail business.
Calgary-based Agrium acquired from Glencore International some 210 Viterra retail stores across Western Canada, in addition to 13 locations in Australia and a minority position in a nitrogen facility in Medicine Hat, Alta., for $1.15 billion.