HOUSTON — Floodwaters in two Houston neighborhoods have been contaminated with bacteria and toxins that can make people sick, testing organized by The New York Times has found. Residents will need to take precautions to return safely to their homes, public health experts said.

It is not clear how far the toxic waters have spread. But Fire Chief Samuel Peña of Houston said over the weekend that there had been breaches at numerous waste treatment plants. The Environmental Protection Agency said on Monday that 40 of 1,219 such plants in the area were not working.

The results of The Times’s testing were troubling. Water flowing down Briarhills Parkway in the Houston Energy Corridor contained Escherichia coli, a measure of fecal contamination, at a level more than four times that considered safe.

In the Clayton Homes public housing development downtown, along the Buffalo Bayou, scientists found what they considered astonishingly high levels of E. coli in standing water in one family’s living room — levels 135 times those considered safe — as well as elevated levels of lead, arsenic and other heavy metals in sediment from the floodwaters in the kitchen.