In a letter to company CEO David Ratcliffe Wednesday, Riley said he was surprised to learn that the head of Southern subsidiary Georgia Power was leading a Georgia "impact team" formed by Gov. Sonny Perdue to work on the state's strategy in the dispute, including lobbying Congress.
Riley said having Georgia Power align with Georgia's interests is "counterproductive."
Along with Georgia Power, Southern owns Alabama Power and northwest Florida's Gulf Power, putting it in a tricky position as the states fight over rivers they share. The utilities are among the region's largest water users.
"Based upon your prior statements about each of the states in which your companies operate having legitimate interests, I had expected that Southern Company would remain neutral and not employ its lobbying group to seek to promote the interests of one of the states," Riley wrote to Ratcliffe. "This sort of out-front advocacy is only likely to harden the negotiating positions of the states."
Spokeswoman Valerie Holpp said Southern Co. had no comment on the letter.
Alabama, Florida and Georgia have been fighting for 20 years over rivers they share.
Georgia wants to hold more water back in federal reservoirs such as Lake Lanier to use as drinking water for the fast-growing Atlanta region. Florida and Alabama say they need strong river flows to sustain their own drinking water needs, fisheries, industrial users and power plants - including an Alabama Power nuclear plant.
In a potentially devastating blow to Georgia, U.S. District Court Judge Paul Magnuson ruled earlier this month that the state has no legal rights to Lake Lanier, a federal reservoir that provides drinking water to some 3 million Atlanta-area residents. Magnuson gave Georgia three years to continue using the reservoir but said if Congress hasn't approved a settlement by then, most of its withdrawals must end.
While taking a neutral public position, Southern Co. has been a key player in the water negotiations. As negotiations heated up last year, the company was included in a confidentiality agreement that the states signed to protect details from public disclosure.