The Chesapeake Bay’s ecological health improved slightly last year, according to a new assessment, with three of the estuary’s key fish populations in their best shape in decades.

For the fifth straight year, the Bay’s condition in 2016 earned a C grade on the annual report card produced by the University of Maryland Center for Environmental Science. The overall score — combining measures of water quality, habitat and fish abundance — ticked upward to 54 percent, a 1 percent gain over 2015.

While not a huge improvement, the score is the second highest the Bay has earned since the annual assessments began in 1986, with only 2002 rating slightly higher. The scientist overseeing the report card said he takes heart from that, and the fact that the Bay’s health has held steady in recent years despite many pressures on it, both natural and manmade.

“I’m more optimistic than I’ve been in a long time,” said Bill Dennison, vice president for science applications at UMCES. “This seems to be sustained.”

The improvement seen by the UM scientists agrees with a report card issued earlier this year by the Chesapeake Bay Foundation, which upgraded its assessment of the estuary’s health from a D to a C-minus. And, the annual Bay Barometer released by the state-federal Bay Program also found many key indicators ticking upward, though it did not give an overall grade.

Bay health has tended to vary with the weather, and water quality, in particular, fares better in drought years. Less precipitation washes less nitrogen and phosphorus off the land to feed algae blooms and lower the dissolved oxygen in the water that fish need to breathe.

But Dennison said he’s seeing evidence that the Bay’s water quality is holding its own, even in years when precipitation approaches normal. He suggested that’s likely the result of Baywide efforts to reduce nutrient and sediment pollution.

Bay grass abundance has improved, and the oxygen-starved “dead zone” that forms every summer in the deepest part of the estuary has shrunk in recent years, Dennison noted.

The UMCES assessment rated fisheries health at 90 percent last year, up from 73 percent in 2015 and the highest score ever. That grade represents an average assessment of abundance for three key species — striped bass, blue crabs and Bay anchovies. Other important species, such as oysters and American shad, remain in doubt, Dennison acknowledged.

Water quality earned mixed scores in the report card. Dissolved oxygen and phosphorus improved, while nitrogen pollution worsened, and the abundance of bottom-dwelling worms and other marine life declined some. And while the “dead zone” in the Bay may have shrunk, dissolved oxygen levels in its tidal tributaries remain a concern.

Water clarity, which had been in a long-term decline, has improved noticeably in the last couple of years. Clearer water has been most pronounced in the central region of the Bay, Dennison said, including tributaries such as the Choptank and Severn rivers.

Dennison said he was heartened by the improvements seen in some of the Chesapeake’s most distressed tributaries. The Patapsco and Back rivers by Baltimore, and the Elizabeth River in Norfolk, all of which once rated F grades, got Ds last year. Only the Patuxent in Maryland and York in Virginia showed no gains last year.

The Bay still has a long way to go to be considered fully restored, he said, but from what he’s seen, he is confident that if the Bay cleanup continues on its present course, even the Chesapeake’s least healthy tributaries will get better.

“We’ve moved that patient from critical condition over to the ICU.”