The author must be thinking of multiple locations within the body of water.
If a single location was meant, you could say
The oxygen level near the waste pipe is low
but you could
not say
* The oxygen levels near the waste pipe are low
You could say
The oxygen levels throughout the lake are low, especially near the pipe, where the level is the lowest it has ever been.
or
The oxygen levels are low in the entire lake, except near the four purifiers, where the levels remain healthy.