Like Florida’s Everglades, the unique “River of Grass,” many of the state’s other rivers are also beset by pollution and fluctuating water levels thanks to seasonal droughts and increasing demand for drinking water in urban areas. Unlike the Everglades, however, many of these threatened rivers are getting no relief. So says a year-long study, Down by the river, of 22 rivers statewide conducted by the Orlando Sentinel.

From the Apalachicola River in the Panhandle to the Miami River in the heart of the state’s largest urban core, Florida’s waterways, which stem from springs and lakes and often intersect, need more help. There are no quick fixes, and certainly no cheap remedies. The state doesn’t completely neglect its abundant waterways — Florida taxpayers already send more than $1 billion a year in fees and taxes to several state agencies that regulate waterways. But all who understand the dimensions of the widespread pollution say much more money will be needed over time.

Largely because of the expense, the state has spent 14 long years resisting the federal Environmental Protection Agency’s 1998 requirement that states write water-quality controls with effective measures to curb pollution in their rivers, lakes and other waterways by 2004.

Florida balked, citing enormous costs, with state officials and EPA bosses in a perpetual sparring match. The state missed the 2004 deadline, and in 2008, exasperated environmental groups sued the state in federal court, citing the federal Clean Water Act. Finally, under court pressure, the EPA agreed to write the rules and impose them on Florida, which continued to resist. But in what is largely seen as a bit of election-year politicking, the EPA in late 2011 backed off, saying the state could write the rules after all.

Still, Florida officials, citing huge compliance expenses for urban areas, industry and agribusiness, resisted. And all the while, the state’s waterways grew more nasty things like algae blooms and dead zones, as runoff of every kind continued. But the end of this battle may be in sight. Last month, U.S. District Judge Robert Hinkle denied the state’s request for more time. He ordered the EPA to implement its water-quality rules in Florida.

What the state does next is anybody’s guess. But what it should do is comply with the judge’s ruling. This will not be easy, yet it’s vitally necessary if the state is to protect its drinking-water supply, which come from waterways, springs and underground aquifers. The costs are high, but the stakes are higher. If Florida is to continue to attract new business investment and residents it has to safeguard this most fundamental basic need of existence.

There are some ongoing efforts to protect and restore some waterways. In the 1980s, the Save our Rivers program bought nearly 2 million acres of open space to protect river basins. The restoration of the historic, north-flowing St. Johns River is one of the state’s most ambitious environmental projects. So is the restoration of the Kissimmee River to its traditional ox-bow flow by the U.S. Corps of Engineers . The cost for both restorations totals $2.5 billion so far.

And then, of course, there is the 20-year plan to restore the Everglades, which is an example of how the state’s waterways are interconnected. The Kissimmee River, located north of Lake Okeechobee, dumps polluting nutrients and urban runoff into the lake, which in turn dumps them into the Everglades and magnificent river estuaries on both coasts of Florida. Cleaning up the Kissimmee is as necessary a step toward Everglades restoration as all the other related cleanup projects in the Comprehensive Everglades Restoration Plan.

It’s also an example of how complex the state’s waterway systems are and why cleaning up and protecting all the state’s water bodies from further pollution can’t be avoided any longer.