The annual water quality grades for the three rivers that flow into Boston Harbor — the Charles, Mystic and Neponset rivers — were released on Thursday, revealing a mix of progress and sliding scores across the region.

In the Charles River, EPA grades ranged from A’s in the upper and middle watershed, B’s in the headwaters and Lower Basin, and a C in the Muddy River.

Some areas saw grades drop slightly due to various factors, according to environmental officials. They noted that increased rainfall, drought, and heat from climate change has led to combined sewer overflows (CSOs), stormwater pollution, low water levels, and toxic cyanobacteria blooms.

The upper watershed fell from a B+ in 2021 to a B last year, the upper middle watershed decreased from an A in 2021 to an A-, and similar trends were seen in the Stop River (B+) and Lower Basin (B).

The Muddy River’s grade improved from a C- to a C. But a C grade is still not acceptable, the officials emphasized, and the Muddy remains the most polluted above-ground tributary within the Charles River watershed.

“While we’ve made such amazing progress since 1995, the work is not done until residents can experience the joy of swimming in cool, clean urban rivers on a hot day,” said Emily Norton, executive director at the Charles River Watershed Association.

“We have the solutions we need, the strong foundation of decades-long federal, state, and local partnership, and the passion and dedication for cleaner rivers — we just have to get to work, with urgency,” Norton added.

In the Mystic River watershed, water quality remains consistent with previous years.

Upper Mystic Lake (A+) continues to have high swimmability, the mainstem of the Mystic River has generally good water quality, and a number of tributaries — including Alewife Brook (D) and the Malden River (D) — continue to show poor grades. Those D grades are due to sewage contamination, especially in wet weather.

“In wet summers like the one we are currently experiencing, and most dramatically in 2021 when 14 inches of rain fell in July, CSO releases are a commonplace occurrence — routinely exposing river users to bacteria, trash, and more,” said Patrick Herron, executive director at the Mystic River Watershed Association.

“We understand that the elimination of remaining CSOs will be expensive — but we believe investment in public health and safety for all communities is worth it, given these discharges inhibit residents from fully enjoying vital greenspaces and riverways,” Herron said.

In the Neponset watershed, water quality remains quite good in the mainstem, receiving A’s and B’s, with three of four sections improving slightly last year. Numerous lakes and ponds received high marks for swimmability, with the highest grades in Turner’s Pond (A+), Crackrock Pond (A+), and Willett Pond (A+).

However, many tributaries have seen water quality worsen, likely reflecting the impact of extreme weather like drought and increased precipitation, officials said. The waterbodies with the worst grades were Meadow Brook (F), Germany Brook (D-), and Unquity Brook (D-).

“Polluted stormwater runoff from streets continues to be a huge problem, and we are working to educate residents and upgrade stormwater infrastructure systems to reduce pollution and prepare for climate change,” said Ian Cooke, executive director of the Neponset River Watershed Association. “We need to slow the flow of stormwater, replenish the groundwater, and return clean, filtered water to our rivers.”