It took decades, generations even, to taint the water of some of the Charleston region’s most popular and visible waterways, so we should expect efforts to minimize the pollution there to take time, too. But our patience should not be unlimited.

The good news is the S.C. Department of Health and Environmental Control recently took a promising step toward cleaning up these waterways by rewriting an older, somewhat puzzling regulation to provide a more accurate assessment for those who swim, kayak and fish in our scenic but troubled waterways. We hope the agency’s action ultimately provides both additional encouragement and assistance to those working to improve coastal water quality.

The change holds all recreational saltwater bodies to the same standard for bacteria counts. Previously, certain waterways, such as Shem and James Island creeks, were allowed to have 80% more bacteria than bodies of water in the other category, such as the Ashley River. The state of South Carolina classifies tidal saltwater bodies differently, with Class SA including areas such as the Ashley, while Class SB includes Shem and Wappoo creeks and the entire Charleston Harbor. The latter were allowed to have 5 times as much bacteria, even though they’re not much different in any practical, recreational sense. And that made no sense.

The state does not close waterways when bacteria counts are high, but it will issue advisories about harvesting shellfish. It’s up to recreational users to be mindful of the risks they face. Leslie Lenhardt of the South Carolina Environmental Law Project told reporter Shamira McCray that the different standards masked the threat the waterways posed, noting that Shem Creek is relatively more polluted, “but it wasn’t triggering a violation.”

Much of the contamination comes from stormwater runoff containing pollutants such as gasoline and pet waste. In some cases, aging and failing septic tanks along the creeks contribute to the problem. The prime issue is the level of enterococci, which live in the intestinal tracts of humans and animals. Too high a concentration in a waterway can sicken swimmers and those who eat raw fish from there.

Andrew Wunderley, Charleston Waterkeeper’s executive director, was among those who pushed for the change, which he called “a little tweak that has a big impact for water quality.” While local officials realize the challenges they face with Shem and James Island creeks — and are working to tackle them — DHEC’s regulation change should add urgency to those efforts. The James Island Creek Task Force already is working on a multi-jurisdictional watershed management plan that it hopes will help secure funding for water-quality projects, such as eliminating septic tanks.

As we’ve noted before, the town of Mount Pleasant needs to encourage more waterfront homeowners along Shem Creek and elsewhere to tap into its sewer system, as do the town of James Island, the city of Charleston and every other coastal municipality. The upfront costs to property owners can be several thousand dollars, but utilities, which are getting new sewer customers, are sometimes willing to help. And increased awareness about risky water quality also adds urgency that could benefit efforts to get grants. DHEC’s next step should be helping to identify pollution hot spots and offering a mix of carrots and sticks to get more waterfront residents off septic tanks.

Future generations will be thankful.