Glen Haven Beach in Sleeping Bear Dunes National Lakeshore. PHOTO: Melissa Downs
Published September 25, 2025
The last days of summer bring quiet changes along Michigan’s shoreline. Crews with the Department of Natural Resources have begun removing bright swim buoys and colored flags that, for months, have marked safe swimming zones at state park beaches.
For many visitors, this signals the end of beach season. But for public health officials, researchers, and community leaders, it’s the start of another cycle. The work of testing water quality and tracking contamination continues well into the fall.
How Michigan monitors its beaches
Michigan has one of the most extensive beach monitoring programs in the country. According to the Department of Environment, Great Lakes, and Energy (EGLE), local health departments regularly monitor about 400 public beaches per year, with results reported through the state’s online Beach Guard system. Sampling focuses on E. coli bacteria, which is a strong indicator of fecal contamination.
Shannon Briggs, Toxicologist with the Michigan Department of Environment, Great Lakes, and Energy (EGLE). Courtesy PHOTO.
Shannon Briggs, a toxicologist at EGLE, explained Michigan’s three standards for testing: if daily results average more than 300 E. coli per 100 milliliters of water, the beach is unsafe for swimming; if the 30-day average of a beach is over 130 E. coli per 100 milliliters of water, that’s also a warning sign; and if a single test hits 1,000 E. coli per 100 milliliters of water, it’s considered unsafe to even wade.
In July 2025, Environment America analyzed a subset of roughly 200 Michigan beaches for its annual Safe for Swimming report, and found that 108 experienced “At least one day on which indicators of fecal contamination reached potentially unsafe levels.”
Briggs cautioned that the report can be misleading, as it fails to cover all Michigan beaches and relies on single samples rather than the geometric mean required under state law. Michigan calls for at least three samples to be collected and averaged from any given beach, which provides a truer picture of water quality. “A single high sample might not mean the whole beach is unsafe,” Briggs said. “By averaging multiple samples, we get a more accurate assessment of the real risk.”
Briggs noted that when Michigan’s testing does confirm unsafe conditions, rainfall is often the leading cause of elevated bacteria levels.
“Rain significantly impacts beach water quality by washing contaminants into the water,” she said. When heavy storms force pollutants from fields, streets, and septic systems into nearby rivers and lakes, bacteria levels can spike quickly, forcing beaches to close.
These patterns continue into the fall season where rainfall remains high before decreasing during the winter months.
Rapid testing improves water monitoring
To improve monitoring speed and accuracy, Michigan created the Michigan Network for Environmental Health & Technology (MiNet) in 2015. MiNet is a partnership of university labs and local health departments that monitor recreational water quality, SARS-CoV-2 in wastewater, and identify sources of fecal contamination in surface water. The network uses rapid DNA-based methods to produce results within hours instead of days.
Erin Dreelin, Professor and Associate Director of the MSU Water Alliance.
“Until recently, Michigan relied on culture-based methods that took 24 hours to return results. That delay often meant advisories came after swimmers had already been in the water,” explained MSU Professor and Associate Director of the MSU Water Alliance, Erin Dreelin. “Rapid molecular methods, especially qPCR, now allow us to provide same-day results and even track the source of contamination.”
The quick turnaround means health departments can act faster during the summer. The same data is then used to identify continued sources of contamination, including septic system failures and stormwater runoff that affect Michigan’s waterways in the fall.
Tracing contamination to failing septic systems
Michigan’s waters remain active well after its shoreline grows quiet. Anglers handle fish caught in rivers and along the Great Lakes, kayakers and canoeists navigate waterways after heavy rains, and families bring their dogs to walk and play at the edge of the water. But the same rivers and lakes that invite recreation are also where signs of pollution show up most clearly. Monitoring points to stormwater runoff, aging infrastructure, and often failing septic systems.
“When septic systems fail, they can release bacteria and nutrients directly into nearby streams and lakes,” said Tanya Rule, who supervises EGLE’s Onsite Wastewater Program. She noted that heavy rains can overwhelm older or poorly designed systems, carrying untreated waste into waterways.
Replacing a septic system can cost around $20,000, Rule said, making it out of reach for many of the 1.3 million homes and businesses that rely on them in the state. In response, EGLE and Michigan Saves launched a $35 million septic replacement loan program in 2024 to help homeowners cover the costs of replacing failing systems and reduce the flow of untreated waste into Michigan’s waters. “So far, we’ve distributed about $4 million and received more than 400 applications,” she said.
Even with that support, Rule noted that financial assistance alone cannot solve Michigan’s broader septic challenges. Michigan remains the only state without a residential septic code. While commercial systems are regulated, oversight for homes varies by county. Monitoring data that consistently links bacteria spikes to failing systems can help make the case for infrastructure funding and future statewide reform.
From monitoring to management
Briggs noted how Michigan’s monitoring program has shaped solutions in the past. Federal funding through the Great Lakes Restoration Initiative, for example, supported redesigns at problem beaches, added vegetated buffers, and helped control wildlife that contributed to contamination. These projects show how monitoring data can guide where money is allocated and where effort goes.
Rule made a similar observation, adding that “Monitoring tells us where systems are breaking down. Without that data, it’s much harder to justify needed change.”
Dreelin added that the value of monitoring depends on the credibility of the results. Networks like MiNet, she explained, make this work possible by standardizing testing across the state. “By training local labs and health departments, we make sure the results are consistent and credible,” she said. “That consistency allows the data to be used not just for immediate responses, but to support bigger decisions about infrastructure and water management.”
Monitoring continues beyond beach season because the conditions that drive contamination—rainfall, runoff, and failing septic systems—continue throughout the year. Fall sampling shows where contamination remains, provides the evidence needed for infrastructure funding, and helps keep problems from cycling back the next year. For Michigan’s public health officials, researchers, and community leaders, each test taken after Labor Day is part of preparing for cleaner, safer waters ahead.
Story by Aja Witt