The EPA took its first step to alter how it tallies the costs and benefits of pollution rules, in a bid to address concerns from regulated industries. That includes how it accounts for the benefits from pollutants that aren’t directly regulated.

“Many have complained that the previous administration inflated the benefits and underestimated the costs of its regulations through questionable cost-benefit analysis,” Environmental Protection Agency Administrator Scott Pruitt said in a statement. The agency released an advance notice June 7 seeking comment on how the EPA should reframe its cost-benefit calculations.

Chief in the EPA’s sights is how...