Baltimore’s Inner Harbor and the streams that feed it became cleaner last year, though they still struggled with high loads of bacteria from leaky sewer  pipes and salinity from road salt.

The Baltimore Harbor’s score reached a high of 55 out of 100possible points, compared to 43 the year the Waterfront Partnership began measuring the harbor in 2012. The tidal Patapsco River did even better, reaching a 57, up from  40 in 2012. The Gwynns Falls wasn’t measured in 2012, but it had a 59 in 2013 and this year went up to a 62.

Only the Jones Falls declined, with a score of 51 as opposed to the 57 it scored in 2013.

The improved scores come even as Baltimore endured 53 inches of rain last year - far more than the 42-inch average. Rain washes more runoff into local waterways through the stormwater system. Unlike many other cities, which have a combined sewer system, the stormwater in Baltimore is separate and untreated. But heavy rain can overwhelm the sewage system, which has old, leaky pipes, and result in more sewage reaching the waterways.

Adam Lindquist, manager of the Healthy Harbor initiative, said the scores show that monitoring the Harbor is worthwhile. Progress is incremental, he said, but before 2013, the Waterfront Partnership didn’t have a baseline from which to improve. Now, he said, the group understands it needs to monitor sites, and do it consistently.

“On the Gwynns Falls, it’s wonderful to see a waterway moving in the right direction,” he said. “It makes you feel good to have your fist water body not receive a failing grade.”

Part of what helped the Gwynns Falls may have been a Baltimore County restoration project on Scott’s Level Branch, which restored 3 acres of filtering wetlands, Lindquist said.

Halle Van Der Gaag , executive director of Blue Water Baltimore, said environmental leaders have to be cautious about pointing to one event in complex systems  as the thing that made the difference.

“It’s hard for us to say 100 percent. - (The Scott’s Level wetlands are) just one project. It’s a very important project,” she said, adding, “We are feeling good that things are heading in the right direction.”

Both Healthy Harbor and Blue Water Baltimore have programs in place to remove trash, green alleys, plant more trees and encourage residents to have a greater role in stewardship. The trash wheel on the Jones Falls has drawn international attention, and plans are in place for a second wheel in Canton. Blue Water Baltimore runs canoe-and-scoop cleanup programs, while Healthy Harbor is focusing on getting people out in kayaks and canoes to help create a demand for clean water.

But huge obstacles remain. Baltimore may not have a combined sewage problem, but it has antiquated infrastructure that requires constant maintenance in tight budgetary times. According to Blue Water Baltimore, the harbor watershed experienced 586 total sewer overflows. Just one of those - August 12, 2014 - contributed 12 million gallons in one day.

Baltimore is not the only city grappling with both polluted waters and a desire to get people out on them, albeit safely. Chicago struggles with sewage overflows into its namesake river, but the city encourages kayaking on it. Pittsburgh, once struggled with major pollution from its steel plants, but now encourages kayaking on its three rivers. Boston, where the harbor cleanup has been fairly successful, has a famous swimming event in its harbor.

On the one hand, Lindquist said, you want people to be safe. But on the other, if you wait for the waters to become pristine, you will never get people using them.

“It makes me very happy to see people out using the waterways, because that will help promote a culture change in Baltimore,” Lindquist said. “That’s what happened in Chicago. There was this popular movement of people seeing the river as recreation. And the politicians said, ‘now there’s so many people out there using this river, I guess we better clean it up.’”