In areas where the groundwater is vulnerable to nitrate contamination, following nitrogen fertilizer best management practices (BMPs) alone may not be enough to reduce the amount of nitrate leaching into groundwater to meet water quality goals. In these cases, the MDA encourages farmers to consider practices and activities that go beyond traditional nitrogen fertilizer BMPs. These are referred to as Alternative Management Tools (AMTs). In many cases these practices are developed and used by farmers and implemented in ways that are relevant for local conditions and opportunities. The MDA will work with the local agricultural community to encourage and incentivize these practices. The MDA will also continue to work toward providing technical and financial resources regarding the effectiveness of these alternatives.

Under the Groundwater Protection Rule approved AMTs may be used as a substitute for the adoption of specific nitrogen fertilizer BMPs within individual Level I and Level 2 Drinking Water Supply Management Areas (DWSMAs). Additional information on specific substitutions can be found on the Approved AMTs page.   


The MDA, in consultation with the scientists at the University of Minnesota and others, is currently reviewing scientific research and writing AMTs.

In addition, the MDA is accepting proposed AMTs for review. The scientifically rigorous AMT review process includes documentation of expected nitrate leaching loss reductions, a review of the scientific literature, consultation with Land Grant university experts, input from the agricultural industry and commodity group leaders, computer modeling and other relevant information, such as research trial data.

AMTs which are approved will be posted on the Approved AMTs page.

Approved and Possible AMTs

The list of approved and possible AMTs below is not intended to be an all-inclusive list, but rather examples of activities the MDA may consider as alternative practices. There may be other practices that the MDA would consider on a case-by-case basis. Individuals are encouraged to suggest new AMTs to be evaluated and added to the list. See the AMT review process to learn how to suggest a new AMT.

Farmers have many choices of alternative practices that may fit into their operation. All of these have one thing in common: they can reduce nitrate-nitrogen leaching and reduce the inherent risk of nitrogen loss.

Many of these practices have well documented reductions for nitrate-nitrogen leaching. Specifically, they can reduce nitrogen input needs and /or increase overall uptake of nitrogen making less available for leaching. For some alternative cropping systems, the AMTs may be conditional as they require already-established BMPs to be followed, such as, using nitrogen fertilizer recommendations from the University of Minnesota.

Alternative cropping systems or low nitrogen input crops can reduce nitrogen input needs and/or increase uptake of nitrogen. Increasing continuous cover can be accomplished by diversifying crop rotations, adopting perennial cropping systems, and incorporating cover crops. 

  • Crops with low nitrogen application needs and land cover
    • Perennial forage (alfalfa, clover, grass pasture and others)
    • Pasture and hayland
    • Crops with relatively low nitrogen requirements, such as small grains (e.g., wheat, oats, rye, barley, triticale) and canola
    • Cover crops
    • Perennial grains
    • Other multiple cropping rotations such as double cropping, relay cropping, inter cropping
    • Forever Green crops and other innovative crops and cropping systems that have the potential to be the next generation of low nitrogen input or nitrogen management crops.
  • Set-aside programs – continuous cover
    • Conservation Reserve Program (CRP)
    • Conservation Reserve Enhancement Program (CREP)
    • Reinvest in Minnesota Program (RIM) (conservation and wellhead protection easements)
    • Land swapping to relocate high-intensity crops from vulnerable areas to a less sensitive location
    • Land retirement
  • Precision agriculture is a method of farm management that uses site specific information on soils, crops, nutrients, pests, and/or moisture to adjust practices to reflect in-field variability. It encourages better management of nitrogen fertilizers and other inputs. Aspects of precision agriculture that improve nitrogen management include:
    • Variable Rate Technology (VRT) - also called precision application or prescription nutrient application
    • Soil grid sampling (generally acceptable for non-coarse textured soils)
    • Selection of lower nitrogen requiring seed and adjusting seeding density
    • Field or sub-field scale nitrogen requirement prediction tools
    • Data gathering and analysis (e.g., weather stations, soil moisture, crop stress evaluation, yield data)
  • Variable rate irrigation water management
  • Crediting nitrogen from irrigation water
  • Conservation tillage or residue management
  • Other university and industry adopted tools and programs
  • Equipment – robots, highboys, drones, others
  • Data gathering and interpretation software and equipment
  • Use of crop sensors to determine nitrogen crop needs
  • Seed hybrids – through selection of crop varieties that have been shown to use nitrogen more efficiently, or allow greater nitrogen uptake
    • reduced nitrogen input varieties,
    • drought tolerant varieties,
    • new varieties with traits that can increase nitrogen uptake (e.g. expanded root systems, nodulation)
  • Use of soil, plant and/or fertilizer amendments that have been demonstrated effective under similar cropping and climatic conditions

Enrollment in the Minnesota Agricultural Water Quality Certification Program

A combination of practices protecting water quality is normally required to be certified through the MAWQCP. Obtaining certification is therefore considered adequate and appropriate as an alternative practice.


The MDA will identify opportunities to collaborate with other agencies, industry, and non-governmental organizations through existing programs and develop new partnerships to foster the development and establishment of alternative practices that address nitrogen fertilizer management.