For many of the fish in the Baltimore harbor, the Day of Judgment is here — again.

Inner Harbor tourists gawked at the aftermath Tuesday: thousands of dead Atlantic menhaden floating on the surface.

The aquatic annihilation — and its lingering stench — is a reminder of the challenges facing the harbor and the broader Chesapeake Bay.

State regulators say no single pollution event caused this fish kill, but point instead to decomposing algae and other organic material — the result of widespread nutrient pollution from runoff and wastewater overflows that has depleted oxygen in the Chesapeake Bay and its tributaries for decades.

Close to 25,000 fish have died in the event, according to the Maryland Department of the Environment, whose inspectors evaluated the area Monday. The fish kill stretched all the way around the harbor, from Canton through the Inner Harbor to Locust Point, agency spokesman Jay Apperson said.

This week’s carnage comes about a month after a sudden dip in temperatures seems to have triggered two even bigger menhaden die-offs in the harbor. Unseasonably cool late August temperatures helped to deplete oxygen that bay denizens need to survive.

In the first of those events, MDE had tallied close to 61,000 dead fish, almost all of them menhaden, alongside around 400 dead crabs, while another event days later left around 121,000 fish dead.

While data gathered by state inspectors on Monday suggested a seasonal algae die-off, monitoring by harbor advocates and scientists on Tuesday pointed to a return of last month’s culprit: A cool evening that caused water near the surface of the harbor to sink and displace the bacteria-rich waters at the bottom.

When sulfur bacteria in those displaced waters reached the surface, it multiplied in the sunlight, sapping oxygen.

This bacteria turned parts of the harbor a greenish color on Tuesday, said Alice Volpitta, the Baltimore Harbor Waterkeeper for Blue Water Baltimore, a telltale sign of the “pistachio tides” associated with these cool weather turnovers in the water column.

Volpitta said both factors may have contributed to this week’s die-off. The harbor seems to be “trapped in this cycle” of algal blooms and cool weather turnovers that have made this an especially deadly season for local fish, she said.

Last month’s fish kills were among the largest in MDE’s records, which date back to 1984.

According to data provided by the agency last month, other substantial fish kills in the harbor include one over the July 4th weekend that claimed at least 8,000 fish, another in September of last year that killed about 24,000, and a 2012 incident that resulted in around 25,000 dead fish.

Sometimes called “the most important fish in the sea,” menhaden are tiny, silvery fish that swim near the bottom of the Chesapeake Bay’s food chain. They tend to travel in large schools.

Though their population is rebounding today, it was much higher in the bay a few decades ago, when MDE records show one 1984 fish kill that claimed a million fish.

As for the stinking mess in the harbor, city workers have shoveled dead fish out of the harbor and into bags this week.

Apperson said “Mother Nature – the wind, tides and birds – tends to take care of the rest.

Meredith Cohn contributed reporting to this article.