Water quality variances

A water quality variance is a temporary change in a state's water quality standard for a specific pollutant and its relevant criteria, allowing deviation from meeting a water quality-based effluent limit (WQBEL) for a particular discharger. Federal and state regulations afford the flexibility to adopt a variance in some situations. For example, a discharger may be uncertain if it can ultimately meet permit limits and either wants to more fully assess its ability before investing in expensive controls, or the discharger anticipates less-expensive control technology becoming available in the near term. In these and other situations, variances are appropriate if they meet the criteria and provisions set by U.S. Environmental Protection Agency (EPA) and MPCA. 

The EPA allows states to adopt variance provisions, but has ultimate approval over variances proposed by MPCA. As the agency delegated to implement the Clean Water Act, MPCA may grant variances through the National Pollution Discharge Elimination System / State Disposal System (NPDES/SDS) permit program. Because of this collaboration, MPCA must assess a variance using the same conditions and criteria that EPA uses. This will ensure a smooth processing of variance requests.

Guidance documents

Resources to help determine if a water quality variance is an allowable option for your permitted facility.


Visit the Water permit holders and chloride page for information information on chloride standard variances for wastewater treatment facilities.

Proposed variance

Southern Minnesota Beet Sugar Cooperative (SMBSC)

MPCA has made a preliminary determination to grant approval to variances for water quality standards to Southern Minnesota Beet Sugar Cooperative (SMBSC).

The public meeting will be online-only via Webex on November 5, 2020, starting at 4:30 p.m. and ending after the presentation and questions can be fielded.

File Webex: Public meeting - November 5, 2020 (4:30 p.m.)

Public meeting on the proposed water quality standard variances for Southern Minnesota Beet Sugar Co-op.
Meeting number (access code): 146 720 1685; password: t52TUr6megp
Join by phone: 415-655-0003; Access code: 146 720 1685

Alexandria Lake Area Sanitary District (ALASD)

MPCA has made a preliminary determination to grant a variance to Alexandria Lake Area Sanitary District. 

MPCA held a public meeting on this chloride water quality variance and fielded questions.

Active variances

This list provides details on variances in National Pollutant Discharge Elimination System/State Disposal System (NPDES/SDS) permits issued by the MPCA. This list is updated annually by October 1.

Pollutant (or Restriction) for which variance is granted: Chloride
Rule citation: 7050.0222, subp. 2, Total Chloride
Receiving water: Spunk Creek
Date approved: 2/25/2020; permit issued 3/15/2020 (limits and monitoring effective 4/1/2020)
Restrictions in lieu of pollutant limit/restriction: Chloride Investigation & Minimization Plan due 180 days after issuance that includes iterative process to identify sources and incorporate source reduction measures. Alternate limits apply throughout the variance term (15 years) to be updated every 5 years based on re-evaluation (40 CFR 131.14(b)(1)(iii)).

Permit ID: MN0042579
Pollutant (or Restriction) for which variance is granted: Total Hardness (Ca + Mg as CaCO3), Specific Conductance, Total Dissolved Solids, Bicarbonates
Rule citation: 7050.0212 subp. 6 and 7050.0222 subp. 7B
Receiving water: Unnamed creek, headwaters to Bob Bay (Birch Lake)
Date approved: 7/25/2000
Restrictions in lieu of pollutant limit/restriction: Alternate ‘additive toxicity’ limit for Outfalls SD008 and SD009 applicable during cold weather months. Chronic WET 3x/yr, biomonitoring and fish monitoring, and treatment optimization study.  In 2008 application for permit reissuance, Permittee requested continuation of the variance.  In response, MPCA staff indicated they would likely not be able to support a renewal of the variance.  Since the 2008 application, MPCA entered into a Consent Decree with Cliffs Erie to address alleged noncompliance.  Actions taken by Cliffs Erie in response to the Consent Decree has resulted in improvements in effluent quality such that the requested variance will no longer be needed (i.e., the request will not be processed as part of the future permit reissuance).

Permit ID: MN0044946
Pollutant (or restriction) for which variance is granted: pH
Rule citation: 7050.0224, Subp. 2; 7050.0227 Subp. 2
Receiving water: SD007 - Stream 4 to Manganika Creek. SD009 - Manganika Creek
Date approved: 6/12/1999
Restrictions in lieu of pollutant limit/restriction: Alternate pH limit of 9.3 due to naturally high pH in groundwater (Outfalls SD007 and SD009). Based on application (deemed complete 11/13/2009), Permittee is currently investigating plans to re-route flow, and MPCA has no plans to renew this variance.

Permit ID: MN0040665
Pollutant (or restriction) for which variance is granted: bicarbonate, chloride, sodium, specific conductance, total dissolved salts, total salinity, and chronic whole effluent toxicity (WET) testing requirement
Rule citation: 7050.0223, 7050.0224, 7050.0210
Receiving water: County Ditch 45
Date approved: 12/29/2004 (Renewal Request Pending)
Restrictions in lieu of pollutant limit/restriction: Surface water monitoring, biomonitoring, acute whole effluent toxicity (WET) testing requirements, and Dissolved Minerals Reduction Program. Permit and variances are currently under review due to permit expiration (11/30/2009).

Permit ID: MN0049786
Pollutant (or restriction) for which variance is granted: fecal coliform (year round disinfection) and mercury
Rule citation: 7053.0215 subp. 1 and 7052.0100 subp. 5, respectively (related to pollutants above)
Receiving water: St. Louis Bay (St. Louis River) and Superior Bay to Lake Superior
Date approved: 1/15/2016 (Mercury Variance)
Date granted: 6/21/2016 (fecal coliform and year round disinfection variance)

Restrictions in lieu of pollutant limit/restriction:  Interim mercury effluent limits lower than the previous NPDES/SDS permit; additional mercury monitoring; further investigation of potential mercury removal technologies. Compliance with a fecal coliform limit from April 1 through October 31 of each year; monitoring the SD001 station year-round and requires intervention disinfection limits if monitoring at two drinking water intakes exceed a specified numeric level; evaluate alternative disinfection options.