Miami-Dade County’s patched-up sewage system is yet again due for a much-needed upgrade, but you have to wonder if the County Commission would even consider it if the U.S. Justice Department and the Environmental Protection Agency hadn’t cracked down in May after a series of disastrous sewage spills that unleashed more than 47 million gallons of raw sewage in Biscayne Bay and other waterways.

County commissioners hate raising water and sewer fees. But, faced with a yet another lawsuit and possibly millions of dollars in fines for violating the Clean Water Act, the county has no choice now but to update a system that, in some areas, is nearly 100 years old.

So in the next month or two, county commissioners will be asked to sign off on a $1.5-billion, 15-year overhaul plan, part of a settlement in a consent decree with the two federal agencies. They should give it a resounding Yes vote, but only after experts take a second look at one controversial aspect of the plan: spending millions of dollars to rebuild the treatment plant on Virginia Key.

Critics and environmentalists have long questioned the wisdom of putting a waste-water treatment plant on the picturesque island (just as they wonder why it was a government dump site at one time). Now, say clean-water activists and other supporters of Virginia Key’s habitat restoration, is the time to get rid of that treatment plant once and for all. Their reasoning is that, in 50 years, the land the plant sits on will likely be under water thanks to the effects of climate change.

This is science talking. A U.S. Army Corps of Engineers study shows that with sea levels rising by three feet by 2060, the plant would be inundated. Miami-Dade is one of four South Florida counties that accepted the study’s findings as part of a climate-change compact to reduce the greenhouse gases that are causing the Earth to heat up. Given all this, county leaders should question the proposed $555 million Virginia Key treatment plant investment, weighing it against another option: building a new plant on the western edge of the county. That, too, deserves a look by scientists for any potential ill effects on the Everglades.

Another part of the federal settlement that will be environmentally beneficial — eventually — is the county’s agreeing to the feds’ demand that in 2027 it will stop dumping some 120 million gallons of sewage each day miles offshore in the Atlantic Ocean.

The 15-year plan the commission should adopt includes any number of ambitious projects that will improve the county’s most basic infrastructure. The county proposes replacing or repairing 7,500 miles of decrepit sewer lines. It also plans to install 7,660 linear feet of sewer mains in an industrial area below State Road 112 between 27th and 37th avenues now reliant on septic tanks, and it will upgrade pump stations and other facilities.

The costs, inevitably, will lead to higher water fees to pay for county revenue bonds. But for decades, a majority of county commissioners resisted raising water and sewer rates to realistic levels. This failure eventually brought federal and state government run-ins over sewage spills in the Miami River, the bay and canals, which forced the commission to take action, like it or not, on bringing fees closer to reality.

So here we are again, facing yet another consent decree vs. costly federal lawsuit. There is no question that the county must live up to this latest agreement with the feds to prevent further pollution to its precious bay and many waterways.