But Mike Jennings, a spokesman for PSEG, the New Jersey company that owns the Salem nuclear power plant, the major water user in the estuary, lauded the court's action, saying it supported "rational environmental decision-making that has been used in the states, such as New Jersey, for years."
The case originally involved the Indian Point nuclear plant in New York.
Environmentalists had urged justices to uphold an appeals ruling that found the Clean Water Act does not allow cost to be used when deciding what technology would best minimize environmental impacts.
It could have required an estimated 554 power plants nationwide to install technology that relies on recycled water - such as cooling towers - to cool machinery.
That would reduce water intake, which would result in fewer fish being killed as they get sucked into the system.
All new power plants must use closed-cycle cooling, but many older ones do not.
The Environmental Protection Agency estimates water intakes at power plants kill 3.4 billion fish a year.
Historically, May said, the court has ruled that agencies do not have the authority to conduct cost-benefit analyses unless Congress expressly provides that authority.
The court upheld a Bush administration interpretation and "found that congressional silence amounts to congressional authorization to conduct a cost-benefit analysis," he said.
May said the decision kicked the ball back to the Obama administration, which among other things could pass more specific rules.
Elaine Makatura, a New Jersey Department of Environmental Protection spokeswoman, said lawyers were reviewing the ruling.
Pennsylvania DEP spokeswoman Teresa Candori said officials were "very surprised by the decision" and were analyzing the potential effects.
