Seeley Lake Special Management Area

A Special Management Area is an area of the County where unique circumstances or contamination risk has resulted in MPH adopting specific regulations. There are currently four SMAs within Missoula County:

1. Missoula Wastewater Treatment Plant Service Area: This SMA is in place to notify property owners are within the boundary of City of Missoula planned sewer service area that the ability to use septic systems is limited.
2. The Rattlesnake Special Management Area: MPH applies additional restrictions in this area in order to better protect Rattlesnake Creek, which is a designated potential drinking water source for the city, in the instance that the existing groundwater wells are for some reason not viable. The rules limit density, require advance treatment systems in some areas, and prohibit further subdivision.
3. Roman Creek/Touchette Lane Special Management Area: This area has higher than average rates of bacterial contamination in drinking water wells. The rules limit density to one home per existing lot, prohibits further subdivision and imparts specific well construction and groundwater level monitoring requirements.
4. Seeley Lake Special Management Area: This SMA was established in 2015 to address significant nitrate contamination from septic systems. Creating the SMA was one of the formal ways MPH acknowledges that it is legally obligated to mitigate known contamination and is prohibited from taking any action, including writing septic permits, that might contribute to known contamination. Unlike other SMAs, the rules in this SMA do not directly prohibit new use, increased density or new subdivisions. Rather, they require advanced nitrate-removing treatment units be installed when a new or increased use is proposed.

In 1996, the Missoula County commissioners funded an aquifer carrying capacity study, which identified the sensitive nature of the Seeley Lake groundwater, even when compared with other similarly developed areas of the county without sewer systems. A groundwater study conducted shortly after concluded that the low conductivity, or the degree to which the Seeley Lake aquifer conducts electricity, would lead to elevated nitrate levels in groundwater unless the community managed sewage in a different way.

Since 2004, the Seeley Lake Sewer District has monitored nitrate levels in the groundwater quarterly at three locations. Given the direction of groundwater flow determined in the groundwater study, nitrate concentrations at these sampling points reflect accumulation from the most densely developed areas of town.

Ongoing monitoring suggests the problem is holding steady at best, but is likely worsening, and staff have found violations of contaminant levels for nitrate in groundwater (10 mg/L).

Recently, the Seeley Lake Sewer District has invested resources into extending the network of monitoring wells in the area of concern. They drilled 14 new monitoring wells in 2022, and the new wells have provided useful information. The results show widespread elevated nitrate contamination and more places and tests where the levels exceed the nitrate maximum contaminant levels of 10 mg/L.

In 2024, MPH offered to conduct a groundwater flow direction study, using the new monitoring wells. In addition, MPH will take over the responsibility for testing for a period of about one year. This will not only save the Sewer District money, but it will also provide valuable data that can inform future decisions. This study is ongoing, and will conclude sometime in 2025.

We know, through years of study and research, about the harmful effects of drinking water with high nitrate levels (over 10 mg/L). Most specifically, exposure to these concentrations can lead to methemoglobinemia, or blue baby syndrome. Alarmingly, newer studies show that consuming nitrate at much lower concentrations is associated with decreased liver function, thyroid disease, some types of cancer and birth defects in newborns, including limb deficiency and spina bifida. While most of the homes and businesses in the area of the known nitrate contamination are served by a tested community water system, that’s not always the case. Several people rely on the groundwater for drinking. According to the EPA, nitrates cannot be removed by carbon filters (like Brita filters) or by boiling the contaminated water. In addition, the community water system has a limited ability to expand or allow new connections due to water rights limitations. This means the likely water supply option for proposed new development in Seeley will be the already contaminated aquifer.

The groundwater study shows that the nitrate-laden groundwater moves through the community, accumulating sewage discharge, and eventually intercepts Seeley Lake and the Clearwater River outlet. While the influence of groundwater on the lakes and rivers in the area has not been studied, we can observe the impacts to the lakes and rivers by the fast growth of aquatic vegetation along their shorelines.

Previous studies of this aquifer and existing peer-reviewed studies on how nitrates get into groundwater clearly conclude the elevated nitrate concentrations in the aquifer below Seeley Lake could only be the result of pollution from septic systems. Hydrogeologic studies and USGS projections estimate that the natural concentration of nitrates in groundwater in this region would be between 0.6mg/L and 1.0 mg/L. This is significantly lower than the nitrate levels in the Seeley Lake Sewer District monitoring data. This contamination is not caused by natural processes. There are generally four human activities or conditions that could lead to nitrate contamination in groundwater: concentrated and/or confined animal feeding operations; large-scale, fertilized agriculture operations; nitrate/nutrient discharge from industrial operations; and discharge from septic systems. There are no animal feeding operations, no large-scale fertilized agriculture operations and no industrial discharge sources in the Seeley Lake area, but there are many septic systems.

In 2023, the Sewer District hired a third-party consultant to analyze samples from several wells to determine if the cause of the contamination was from human waste, or some other source. Those results were released in 2024, and every sampled well showed that the contamination was linked to human sewage.

MPH was first made aware of these consistently high nitrate levels in 2011. Both MPH’s mission to protect the environment and human health, as well as their obligation under state law to not issue any permits that could cause or contribute to a violation of an established water quality standard, influenced MPH's next steps. In 2011, a protocol was put in place that required any person proposing a new or increased wastewater source in the area to justify why the proposal would not make the existing problem worse and provide evidence demonstrating the projected increase in nitrate loading would not cause any of the three wells to exceed 10mg/L. Sanitarians were not allowed to issue a permit for a new or increased use unless this evidence was provided.

In 2015, the existing protocol and a defined boundary were adopted into the City-County Health Code, Regulation 1, Section 20, Special Management Areas, which states:

(D) Seeley Lake Special Management Area. The following restrictions apply to land located in the NW quarter of T16 R15 Section 2, the East half of T16 R15 S03, and the South half of T17 R15 S35 (see Appendix G).

(1) New or increased use may not be approved unless the Department determines that it will not cause or contribute to a violation of the nitrate standard established in 76-5-605, MCA.

(2) The Department will evaluate septic permit applications on a case by case basis, using the best information available including, but not limited to, nitrate sample results and existing studies on groundwater flow direction. The Department may require an applicant to supply additional information to substantiate that groundwater will be protected.

(3) Provided there has been no unapproved increased use, replacement systems will be allowed in this area.

When the Missoula City-County Health Board adopted the Seeley Lake Special Management Area regulations in 2015, the Seeley Lake Special District was on its way to implementing a community-wide solution to the contamination. A wastewater management preliminary engineering review was completed in 2012. After community input on the wastewater management options identified in the review, the Sewer District Board members chose to pursue a public sewer system that would collect and transport the community’s wastewater to a treatment plant. The plant would have been capable of reducing nitrate concentrations to levels far below conventional septic systems before releasing the treated sewage discharge to a series of drainfields located outside the nitrate contamination area.

The current SMA regulations in the Health Code were enacted to “hold the line;” a stop-gap measure to ensure the contamination did not get significantly worse while the community solved the problem. The regulations only address proposed new and increased use. This regulatory approach will never result in a decrease in nitrate entering the system, as it does not address or mitigate the existing septic systems that continue to load the sensitive system with nitrate from human waste.

Accomplishing a public sewer project is incredibly challenging. This is the case everywhere, not just in Seeley Lake. Unfortunately, in 2021 after the new sewer proposal was voted down by residents, the Seeley Lake Sewer District Board had to release millions of dollars in grants and loans that had been committed by various funders.

Fortunately, the current Sewer District Board has recently gained positive momentum toward a community-wide solution. Their chosen consulting firm is in the process of evaluating a number of sewer system options for the community and compiling a list of pros and cons in terms of cost, level of treatment and location. The Sewer District, MPH, and the state and county emergency management offices are working together to secure funding for the planning and construction of the chosen sewer system.