RIVERHEAD, N.Y. — The dead turtles, about 100 of them, started washing ashore near here in late April. Then came the dead fish, in numbers no one had seen before. By this week, tens of thousands of fish carcasses had bobbed to the surface of the Peconic River, which runs along the southern border of this town, and in adjoining Flanders Bay, washing ashore in putrid drifts.

The waters of the Peconic Estuary, on the East End of Long Island, were coughing up their fauna.

There is little debate about what caused the die-offs. Scientists trace the fish carnage to algal blooms fed by elevated levels of nitrogen, which can be attributed in large part to the region’s outdated septic tanks and cesspools. Evidence suggests that a similar sequence killed the turtles in what scientists said was a highly unusual die-off.

Nitrogen loading in the ground and surface waters of Suffolk County is a longstanding problem that threatens the area’s natural ecosystem and, by extension, its economy.

“It really is a crisis,” said Anna Throne-Holst, supervisor of the Town of Southampton, on the southern flank of the Peconic Estuary. “It needs all the attention it can get.”