The Valero oil company and Amports, owner of terminals that ship oil products, have agreed to pay $3.3 million to settle a lawsuit by the environmental group SF Baykeeper, which said the companies had discharged petroleum coke pollutants into bay waters outside Valero’s refinery in Benicia. The settlement, approved Monday by a federal judge, includes $2.38 million to be paid to the nonprofit Rose Foundation for Communities and the Environment, which will distribute it to local groups for projects related to water quality. The rest will go to SF Baykeeper for costs related to the lawsuit that it filed in March 2022.  While denying any wrongful acts, Valero and Amports agreed to take steps to improve shipping and loading of the petroleum product, sweep residue from ship decks, regularly test the waters and pay additional sums for any further pollution. Valero will pay $1.5 million of the settlement and Amports $1.8 million.