Nitrogen is continuously cycled within the soil-plant-air system, and its availability is weather-dependent. These natural processes make it difficult to predict exact nitrate losses ahead of time. Nitrate can be present in drainage water at all times of the year that drainage occurs. Most drainage flow and nitrate loss occurs from November to May when crops are not growing. This contrasts with the timing of pesticide loss which mostly occurs soon after application in the spring.

Pesticides generally degrade faster than nitrate and are held more tightly by the soil. Thus, they are less available for transport later in the year. Nitrogen is more likely to remain available in the soil after plant growth requirements have been met. Methods to minimize nitrate loss include managing the rate and timing of nitrogen application, and better management of drainage waters through water table management. Both of these strategies prevent the build-up of excess nitrate in soils during times of the year when plants are not growing and drainage flow is high.