The Bay Program’s latest effort to answer the perennial question — how is the Bay doing? — offers a decidedly mixed view of the efforts taken to help restore the Chesapeake and its watershed.

While it shows pollution reductions proceeding ahead of schedule, it shows most of the Bay and the streams that feed it are still in poor health. And while good strides are being made on some efforts such as fish passages and public access, other important goals — such as planting stream forest buffers — are coming up far short.

The Bay Barometer is an annual report from the state-federal Bay Program that provides an overview of Bay health and restoration efforts drawn from dozens of indicators developed from state and federal monitoring programs and a variety of other assessments. It is meant to help the public track changes in the Bay over time.

The latest report, released in December, includes data largely from 2012, though some 2013 figures are included.

It estimates that the amount of nitrogen reaching the Bay has been reduced by 18.5 million pounds since 2009, achieving 25 percent of the nitrogen cleanup goal; while phosphorus has been reduced by 1.3 million pounds, achieving 27 percent of the goal; and sediment has been reduced by 441 million pounds, achieving 32 percent of the goal.

That would place nutrient reduction and sediment reduction goals well ahead of schedule toward meeting 2025 cleanup goals set in the Chesapeake Bay Total Maximum Daily Load, which establishes the maximum amount of those pollutants that can reach the Bay.

Yet, water quality monitoring continues to show a more muted story. While the majority of monitoring sites along rivers throughout the watershed show downward trends for nitrogen and phosphorus since 1985, in many places those trends have leveled off in the last decade.

And the Bay itself, almost stubbornly refuses to provide a widespread response. Just 29 percent of the Bay and its tidal tributaries met water quality standards during the 2010–12 period (standard attainment is based on a three-year rolling average), a level of attainment that has not varied much over the last decade.

“We sort of hit a glass ceiling — some ups, some downs,” said Rich Batiuk, associate director of science with the EPA Bay Program Office at a media briefing on the report. But, he said some individual areas of the Bay have shown significant improvements. Still, “we have a lot of work to do.”

Nick DiPasquale, director of the EPA Bay Program Office, cited recent reports that showed there are often significant lag times between when actions take place on the land and when they affect water quality.

“Some of the practices we implement will take time before they show their full [pollution] reduction benefits,” DiPasquale said. “That’s important to keep in mind.”

The data also showed that 74 percent of Bay segments were impaired because of toxic pollution, up from 66 percent in 2006.

The report showed that key habitats around the Bay continue to suffer from pollution.

Underwater Bay grasses — important for juvenile crabs and fish as well as waterfowl — declined to 48,195 acres in 2012, a 21 percent drop from the previous year, reaching their lowest level since the mid-1980s.

Just 45 percent of bottom habitats surveyed in 2012 had healthy populations of worms, clams and other benthic organisms. That was the same as the year before, but a bit below the long-term average of 47 percent.

Nearly 60 percent of the streams surveyed in the Bay watershed in 2000–2010 were in poor or very poor condition, the report said.

Some restoration efforts fared better.

The report cited ramped-up efforts to restore oyster habitats, with almost half of the reef construction and oyster “seed” planting goals achieved in Maryland’s Harris Creek by last October. That multi-year project is the largest oyster restoration undertaken in the Chesapeake.

Still, oyster populations in the Bay remain near historic low levels and “it is going to take multiple decades, at best” to see a significant recovery, said Tom O’Connell, fisheries director with the Maryland Department of Natural Resources.

Dam removals or new fish passages reopened 35 miles of river habitat to migrating fish in 2012. That brings the total opened since 1988 to 2,543 miles, which is approaching the Bay Program goal of 2,807 miles by 2014.

Also, 2,231 acres of wetlands were established, or rehabilitated on agricultural lands. That brings the total restored on agricultural lands since 2010 to 5,503 acres.

But only 285 miles of streamside forests were planted in the watershed. That’s an increase from the 240 miles planted the previous year — the lowest figure since riparian planting efforts began in the late 1990s — but significantly less than the Bay Program goal of 900 miles per year.

Several fish species showed positive trends.

American shad, based on data from the Susquehanna, Potomac, Rappahannock, York and James rivers, are showing an upward trend, driven primarily by increases in the Potomac.

The number of female blue crabs in the Bay increased in 2013, up 51 percent over 2012 numbers. The female population is below target levels, but remains above the overfishing threshold and well above levels seen prior to the implementation of new catch limits in 2008 that are aimed at protecting females. “The blue crab resource is doing well,” O’Connell said. “There will still be low periods, but hopefully, they will be shorter.”

Striped bass numbers — based on overall Atlantic Coast population estimates — have been decreasing since 2004, but remain above the overfishing threshold, and the population is eight times what it was in 1985, when low abundance led to a fishing moratorium, O’Connell said.

For people who enjoy the water, there were improved opportunities to get to the Bay and its tributaries. Eighteen public access sites were added, bringing the total number of access sites along the Bay and its tributaries to 1,171. “We think the 2013 figures could well be better than the ones for 2012,” said John Davy of the National Park Service.

People might find more competition for those sites. The watershed population has reached 17.7 million — up from 13 million when restoration efforts began in 1985 — and the report said it is on track to hit 20 million by 2030, putting more pressure on the watershed and the Bay.

The 2012–13 Bay Barometer can be found on the Bay Program website, www.chesapeakebay.net, by clicking on the “Bay Resource Library” tab then selecting publications. The supporting documentation can be found under the “Track the Progress” tab on the website.