Fertilizer Management is Key to Realizing Yield and Water Quality Benefits from Cover Cropping

Authors: Cibin Raj, Marali Kalra

What is the issue?

Cover cropping provides several benefits to agricultural ecosystems, from nutrient retention to soil protection to improved soil fertility. Cover cropping practices, such as the choices of cover crop species, planting and termination times, and termination practices, can affect the benefits. The cost of cover crop implementation is a major obstacle to its uptake among farmers. Watershed-scale studies are needed to explore the benefits and drawbacks of increased cover cropping and to help stakeholders make informed decisions about cover cropping implementation.

The Susquehanna River Basin (SRB) is a tributary of the Chesapeake Bay, where impaired water quality has drawn attention to nonpoint-source nutrient and sediment pollution from agricultural fields in the SRB. Agricultural best management practices (BMPs), including cover crops that reduce nutrient losses from cropland, have become a priority for managing nutrient load to the Bay. Assessing the ecosystem services at the landscape level (on-field), the direct benefits of cover cropping for farmers, as well as the downstream ecosystem services in the Bay, highlight the value of cover crops to SRB farmers. This recognition creates a strong incentive for them to adopt cover cropping practices in their operations.

What did we find and why does it matter?

Increasing the area under cover crop provided benefits to all the on-field ecosystem services: it increased annual average corn-soybean crop yield by 9% at the field level, reduced soil loss, increased the amount of biomass returned to agricultural soil, and increased the recycling of nitrogen and phosphorus to plant-available forms. Although increasing cover-cropped areas reduced annual average sediment and nutrient loads at the watershed outlet, summertime nutrient loads increased as decaying cover crop biomass contributed to summer nitrogen and phosphorus loss.

Figure 1. Barplot showing annual average total sediment, total nitrogen, and total phosphorus loads at the watershed outlet under three different cover crop scenarios: a baseline representing current conditions (cover-cropping implemented on 20% of agricultural lands), an aspirational scenario representing an achievable increase in cover-cropped area (40% of agricultural lands), and an extreme scenario representing the maximum possible cover-cropped area (100% of agricultural lands).

Switching from grain to legume cover crops increased plant-available nitrogen due to nitrogen fixation by legumes. This led to increased corn/soybean yield (yields after grain cover crops were 4% lower than after legume cover crops), reduced soil loss, and increased nitrogen mineralization, with minimal effects on outlet water quality.

Extending the cover crop season protected agricultural soils for longer periods each year, leading to improvements in outlet water quality (3% decrease in annual average sediment load, though effects on nutrient loads were minimal) and better erosion regulation (soil loss decreased 20% in cover-cropped fields, and 2% in the watershed as a whole). However, corn/soybean crop yield decreased (6% in cover-cropped fields) when the cover crop season was extended, likely because of the decreased growing time allowed for regular season crops.

Harvesting cover crop biomass lowered the amount of biomass retained in the soil, which led to decreased nutrient mineralization. Removing aboveground cover crop biomass each spring also caused increased soil loss (5% at the field level), due to the lack of springtime soil protection after cover crop harvest. Corn/soybean crop yields decreased relative to the non-harvested baseline scenario (5% at the field level), likely due to the loss of the nutrients stored in cover crop biomass. However, the harvest scenario also saw decreases in annual average nitrogen and sediment loading at the watershed outlet (-2% each). Furthermore, harvesting cover crops allowed for the production of a small hay crop in addition to the regular season crop in cover-cropped fields.

Figure 2. Field-level annual average results for crop yield and soil loss under various cover cropping practices.

Key synergies

• Increasing the area under cover crops augments the green manure effect: cover crops absorb nutrients that would otherwise have been lost from the soil in winter, improving outlet water quality. Those nutrients are released back into the soil after cover crop termination, where they are mineralized into plant-available forms for corn/soybean crop uptake
• Harvesting cover crop biomass improves downstream water quality while supplying a secondary hay crop

Key trade-offs

• Harvesting cover crop biomass produces an additional hay crop, but negates many of the other on-field benefits of cover cropping by removing soil protection and reversing the green manure effect
• Extending the cover crop season has benefits for both downstream water quality and on-field erosion regulation, soil formation, and nutrient cycling, but it impinges on the regular season crop growing season and reduces corn/soybean crop yields
• Cover cropping without adjusting fertilizer application rates shifts the burden of outlet nutrient loading from winter to summer

What did we do?

Using the Soil and Water Assessment Tool (SWAT), a process-based hydrology and water quality modeling tool, we simulated seven cover cropping scenarios in the SRB. Our scenarios compared on-field and downstream ecosystem services under different levels of cover crop implementation (a baseline level, representing current conditions, where 20% of agricultural lands were cover-cropped; an aspirational scenario where cover cropping was implemented in 40% of agricultural land; and a limiting scenario where all agricultural lands in the SRB were cover-cropped), different cover crop species, and two alternative cover crop practices (extending the cover crop season by planting early and terminating late, and harvesting cover crop biomass).

The ecosystem services we studied are listed in Table 1, together with the SWAT output variables used as indicators for each service. We computed annual averages at the watershed outlet for water quality and at both watershed and field scales for all other services.

Publications completed for this work

Kalra, M., Chiles, R., Kaye, J., Kirchhoff, C., Wainger, L., & Cibin, R. (2025). A systematic review of ecosystem services modeling for environmental health assessment. Ecological Indicators, 172, 113245. https://doi.org/10.1016/j.ecolind.2025.113245

Kalra, M., Cibin, R., & Kaye, J. (n.d.). Cover crop implementation strategies differentially impact in-field and downstream ecosystem service provisioning: A regional case study (Manuscript in review).

Lisenbee, W., Saha, A., Mohammadpour, P., Cibin, R., Kaye, J., Grady, C., & Chaubey, I. (2024). Water quality impacts of recycling nutrients using organic fertilizers in circular agricultural scenarios. Agricultural Systems, 219, 104041. https://doi.org/10.1016/j.agsy.2024.104041

Saha, A., Cibin, R., Drohan, P. J., White, C., & Veith, T. (2023). Environmental benefits of weather-based manure timing and placement strategies across the Susquehanna River Basin. Journal of Environmental Management. https://doi.org/10.1016/j.jenvman.2023.117386

Saha, A., Saha, G. K., Cibin, R., Drohan, P. J., White, C., Veith, T., Kleinman, P., & Spiegel, S. (2022). Evaluation of water quality benefits of manureshed-based manure management in the Susquehanna River Basin. Journal of Environmental Quality. https://doi.org/10.1002/jeq2.20429