A south-central Minnesota ethanol plant is again getting hit with a fine for environmental violations, this time for failing to keep production runoff from polluting nearby waterways and other missteps.

Since 2009, Corn Plus has been fined more than $1.1 million at the state or federal levels, and also was ordered several years back to make nearly $700,000 in environmental upgrades.

The latest fine against Corn Plus totals $39,450 and comes from the Minnesota Pollution Control Agency (MPCA). Along with paying the penalty, the Winnebago-based company has agreed to correct several environmental problems.

The agency found numerous violations of the plant’s stormwater permit that sets conditions to ensure runoff from the facility does not pollute lakes, streams and groundwater.

The violations included: failing to draw test samples from ponds, allowing leaks from its cooling towers, improperly managing the water levels in the ponds, allowing runoff from trash bins, failing to manage industrial waste spilled or dumped at the plant property, and late submissions of records.

In a written statement issued Wednesday, company President Bill Drager said the “compromise agreement … did not require Corn Plus to admit any of the MPCA’s factual allegations, many of which Corn Plus disputes. Rather than continue to challenge these allegations, however, Corn Plus determined it was in the best interests of its member patrons, the community and the environment for it to resolve these issues and move forward.”

MPCA spokeswoman Cathy Rofshus said the agency is not interested in seeing Corn Plus shut down over the repeated violations. “Our goal is always compliance,” Rofshus said.

A battle in 2014 for managerial control of Corn Plus resulted in new leadership. Drager said he thinks the 22-year-old company is better positioned to meet the environmental standards that regulators require.

The current managers “can bring more resources and experience to environmental compliance than we have had in the past,” he said.

Rofshus said the MPCA has “seen better environmental behavior” by Corn Plus under the new leadership, but “is that the result of new management? We don’t know.”

In 2014, Corn Plus was fined $25,141 by the MPCA for venting pollutants into the air for longer than allowed, failing to inspect equipment and keep proper records, and failing to adjust equipment to ensure operation to control pollutants.

In 2011, Corn Plus pleaded guilty to a federal felony charge of falsifying air pollution-monitoring data. It paid a $450,000 criminal fine levied by a federal judge and a separate $310,000 civil penalty imposed by the MPCA.

In 2010, Corn Plus paid a $200,000 fine to the state for water quality violations and agreed to environmental projects at the plant costing more than $690,000.

In 2009, Corn Plus paid a $150,000 penalty as part of a settlement with the U.S. Environmental Protection Agency for criminal charges related to water quality violations.