SAN FRANCISCO (KGO) — While the San Francisco Bay can often look nothing short of magnificent, judging the health of the Bay and the waterways that flow into it is a tricky business. Laura Feinstein, Ph.D., and her colleagues at the San Francisco Estuary Institute and Estuary Partnership have just released a detailed report card, called the State of our Estuary.

“The State of our Estuary looks at the health of the San Francisco Bay and Delta across 24 indicators,” Feinstein said. “And we found that for the Bay, most of those indicators are doing okay and they’re holding steady. But in the Delta, most of those indicators are in poor condition.”

Essentially, a tale of two ecosystems, interconnected. On the positive side, are the years of restoration work. Nearly 60,000 acres of Tidal marsh now surround the Bay shoreline, benefiting several key species of shore birds. Conditions at most Bay beaches also boasted positive water quality.

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“So one of our big findings was where we have seen, managers really take action on the ground, we see the payoff,” Feinstein said. “So, for example, we’ve restored tens of thousands of acres of marshes in the bay and Delta, and we’re seeing the birds that live in those marshes are really thriving.”

But traveling inland to the Sacramento San Joaquin Delta, the report points to man-made changes having the opposite effect. Environmental scientist Tina Swanson, Ph.D., with the San Francisco Estuary Partnership, says freshwater flow through the Delta has been cut nearly in half. This is mainly the result of deliberate diversions for farming, drinking water and other human uses. She says it is a shortfall threatening multiple native fish species, including Chinook Salmon.

“And if the conditions on the Delta are as poor as they are now, very often the survival of the fish through that part of the migration is very low,” Swanson said. “That is one of the reasons that salmon populations have been declining and have reached such low levels now that, in fact, the California Chinook salmon fishery has been closed for years because they’re trying to preserve the few fish that can make it back up to the rivers to reproduce, to sustain the species.”

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Researchers say many parts of the Bay and Delta also share common threats from pollution, ranging from microplastics to toxic chemicals like mercury found in seafood samples. And rather than awarding an overall grade, they see the report card as a call to action, with the added urgency of a changing climate.

“You do see that there’s these big underlying processes. How clean is the water? How much freshwater is there? Is there enough habitat?” Feinstein said. “Those things really drive everything else, like is it safe to swim in the Bay for people or is wildlife flourishing? So if you see the underlying factors doing well, then you start to see everything connected to it doing well and anything we should be thinking about this related to say things like sea level rise, things that we see changing.”

These are improvements to our Bay ecosystem we will still need to pay attention to in the future. This report card is also significant, because it’s the first time the data is being updated in more than five years.