Owners of hydroelectric dams along the Black River, including the city of Watertown, will see a 36 percent increase in the fees that they pay to a state regulating agency that came under financial duress in other parts of New York.

Officials at the Hudson River-Black River Regulating District say the move to raise $313,000 in one year was inevitable, but a state legislator said it was just another example of robbing from Black River communities to pay for problems elsewhere.

“The Black River side is now paying for the mismanagement of the Hudson River side,” said Assemblyman Kenneth D. Blankenbush, R-Black River, who proposed splitting the agency.

The agency controls the flow and level of water on its rivers to prevent the risk of flooding. It receives its operating revenue by charging a fee to hydroelectric dams on the Black River. It used to raise most of its money by charging federally licensed hydroelectric dams on the Hudson River, but in 2008 it lost a court battle to be able to do so.

In 2011, the agency used $3 million in a reserve fund belonging to the Black River portion of the district to make up for the Hudson River portion’s cash flow problems. Each side of the agency has its own administrator and its own board members, and the two sides have separate bank accounts, but a court decision forced the agency to use the Black River side’s money to pay off property taxes owed to Hudson River communities.

The added revenue from the 36 percent fee hike won’t go toward paying any Hudson River expenses, said Michael Clark, the systemwide administrator. Instead, it will go toward refilling the Black River side’s bank accounts, which nearly were depleted after the court decision.

“Unfortunately, it meant for this year an increase in assessments that’s clearly unpalatable,” Mr. Clark said. “I understand. I understand the cost of doing business in this economy. And yet to not have the necessary income would jeopardize the fulfilling of the regulating district’s mission.”

Mr. Clark said that Mr. Blankenbush’s proposal to split the two agencies was not a good idea. The agencies used to be separate, but were combined in the 1950s to reduce overhead costs. The Black River side of the district pays about 20 percent of administrative expenses, which would increase if it were to split into its own agency, he said.

The Hudson River side of the district is now looking to charge the state and five Capital Region counties — Warren, Washington, Saratoga, Albany and Rensselaer — a fee to protect them from flood damage. A court has given the go-ahead for that fee, Mr. Clark said. The agency believes it’s only a matter of time before the Hudson River side of the district is back on its feet again and, by next year, the fees for the city of Watertown and other Black River hydro producers will be reduced.

The hydro producers usually see a small, single-digit increase in assessments, Mr. Clark said, calling the 36 percent hike “unprecedented.”

He said the fee hike was passed at the district’s June meeting.

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