In 1858, sewage clogging London's Thames River caused a "Great Stink." A century later, parts of the famed waterway were declared biologically dead.

But the latest report on "The State of the Thames" is sounding a surprisingly optimistic note.

The river today is "home to myriad wildlife as diverse as London itself," Andrew Terry, the director of conservation and policy at the Zoological Society of London, writes in a forward to the report published Wednesday. Terry points to "reductions in pressures and improvements in key species and habitats."

Among those species are two types of seals. Before the early 2000s, little was known about their whereabouts, but now "[both] the harbour seal and the grey seal can be seen in the Thames," the report notes, from the river's tidal limit west of London, through the center of the city and across its outer estuary.

Another success story pointed to in the report is the avocet, a migratory wading bird which had become extinct as a breeding species in Britain by 1842 due to habitat loss. It began making a comeback after World War II, and over the last three decades has seen its population among the tidal Thames more than double, according to the report.

There are promising trends, but still plenty of caution

The report highlights several promising trends. But it also cautions that work still needs to be done in other areas, and warns of the negative impact of climate change on the river, which is a major source of water for the city.

"Dissolved oxygen concentrations, critical for fish survival, show long-term increases," it says. "Further, phosphorus concentrations, have reduced in both the long and short term, showing the effectiveness of improved sewage treatment works to reduce harmful levels of nutrients entering waterbodies."

The short- and long-term outlook for birds and marine mammals on the river is improving, according to the report. However, it says the situation for fish is deteriorating slightly in the long term. While that could be due to changes in sampling methods, it might also "be an indication of pressures on fish populations either in the Tidal Thames, or further afield," the report says.

The report also cautions that "a long-term increase in nitrate concentrations" could also threaten water quality.

"In addition, the influences of climate change are clearly impacting the Tidal Thames, as both water temperature and sea levels continue to rise above historic baselines," it says. "This will undoubtedly affect the estuary's wildlife, leading to changes in life-history patterns and species ranges."

The report says that the expansion of sewage treatment plants beginning in 1960 and limits on industrial discharges have helped clean up the Thames, to some extent.

"However, because London's sewage system was largely built in the 1800s when London's population was less than a quarter of what it is today, storm events cause excess sewage to overflow into the Tidal Thames, posing a major threat to water quality," it adds.

A 'super sewer' is coming to the Thames to help the estuary

There is a possible fix on the horizon. London is currently building a "super sewer" project, which is called the Thames Tideway Tunnel and is due for completion in 2025.

"Once operational it will capture and store most of the millions of tonnes of raw sewage that currently overflow into the estuary," the report says.

Despite the improvements for the river's water quality, a research paper published last year indicated high levels of microplastics in samples of the Thames water column taken in 2017.

Experiments have shown that such microplastics can have detrimental effects on aquatic life, as well as turtles and birds, according to National Geographic. Among other things, they can block digestive tracts — with some animals dying from starvation when their stomachs become filled with plastic.

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