The LimnoTech machines will monitor stream levels, temperature, dissolved oxygen and turbidity, the Post Bulletin reported.
The south, middle and north branches of the river will be monitored until they meet around Elba.
The state’s Legacy Amendment will fund the $500,000 project, said Neal Mundahl, a biology professor at the Winona State University who is leading the water study.
The study is expected to last two years, but the machines could be reused in other streams, he said.
Researchers will look for chemicals that are created when other chemicals breakdown.
"We are looking for some of those newer ones, the ones that have not been examined too often," Mundahl said.
Thousands of fish were killed after heavy rain in July 2015.
The machines could help researchers identify the source of contaminated water if a contamination occurs.
"We will get tons of data, no matter what," Mundahl said.
"Our goal is never seeing a fish kill, never detect anything really nasty."