Baltimore’s harbor and the streams that feed into it again merited a failing grade on their 2013 annual report card, indicating the waters around the metro area suffer from continued loads of nitrogen, phosphorus, sediment and garbage.

The report card, which is part of the Healthy Harbor initiative of Blue Water Baltimore and the Waterfront Partnership of Baltimore, looks at multiple indicators of human health and pollution, and maps where they are, before giving its grade. Factors include dissolved oxygen, nitrogen, phosphorus, chlorophyll a and water clarity. It also looks at conductivity from chemicals, particularly those laden with salt, and fecal coliform bacteria, which is coming from sewage and septic systems.

Baltimore’s waterways scored poorly in all categories except dissolved oxygen and water clarity. Baltimore’s streams actually scored an A in turbidity/clarity, in part because the cloudiness of a stream is a localized and temporary condition.

Even with the grade of F, the state of Baltimore’s water was better in 2013 than it had been in 2012, which was the first year that the group began monitoring the waterways. In 2012, the harbor scored a 42 percent, compared with 2013’s 51 percent. The tidal Patapsco River improved from 40 percent to 55 percent. Last year, the group did not sample streams; in 2013, they scored 57 percent — indicating they are heading into D territory.

This year, some of the streams in the Gywnns Falls watershed earned a C-minus, but many in both the Gwynns and the Jones Falls still scored an F.

“While a grade of F is a sobering one, we must use this grade to strengthen our resolve,” said Halle Van Der Gaag, executive director of Blue Water Baltimore.

It may not sound like much of a cause for optimism, but those working on Baltimore’s cleanup nonetheless felt encouraged. For decades, little effort was made to clean up Baltimore’s harbor. Regular fish kills were dismissed as a part of life. When well-to-do residents who bought waterfront condos complained about the smell, officials greeted them with a what-did-you-expect shrug, recalled Phil Lee, one of the early advocates of cleaning up the waterway.

But that began to change around 2010, when the Waterfront Partnership swung into action. Led by Laurie Schwartz, a former deputy mayor of Baltimore, and Mike Hankin, president of Brown Advisory, the group not only took over management of the harbor’s walkways and activities but considered cleaning up the waterway to be part of its mission. The business community funds the partnership through a tax that many businesses located on the waterway support. Other harbor businesses, like Constellation, have become involved in cleanups and even started harbor oyster gardens.

The location that the Healthy Harbor group chose for this year’s announcement proved the point that a new generation is reclaiming parts of Baltimore once deemed lost. It took place at Mill #1, a once-industrial building on the Jones Falls which is now home to pricey condominiums that include an infinity pool, fitness center, private parking garage and sweeping views of the river. It’s in the center of Baltimore, within walking distance of Hampden’s shops, yet loaded with natural beauty. And yet, just to the right of the deck where officials stood was an old industrial hulk of a building, pipes at its roof, the better to discharge industrial waste.

Harbor officials like Van Der Gaag see other reasons for optimism. The city’s stormwater fee passed in 2012 and will be assessed soon, allowing Baltimore to make much-needed improvements to its aging infrastructure. Baltimore just installed a new trash wheel that will remove close to a million pounds of trash from the Jones Falls every year. And the city just promoted Rudy Chow, a department head from water resources, to public works director. Chow spent nearly three decades with the Washington Suburban Sanitary Commission.

At a press conference announcing the failing grade, Chow said: “I take personal responsibility and accept it as a personal challenge that we will, one day, get an A in the coming years. That’s my commitment.”

Chow, who has long advocated developing a plan to repair infrastructure before it fails, promised that Baltimoreans would see a “shift in culture from reactive to proactive…we don’t have to wait for it to fail before we fix.”

Hankin said he was particularly encouraged that close to a million people have viewed a video of the Jones Falls Water Wheel. Most of them, he said, were likely young people; The video is available on YouTube and was posted at Reddit.

“The most vocal part of our coalition is just beginning to form,” Hankin said. “This next generation is much more vocal, has much more urgency and will not take no — or wait until tomorrow — for an answer.”