One of the byproducts of the anaerobic digestion process is a liquid effluent. This is a stabilized organic solution that has value as a fertilizer, and other potential uses. For this reason, the effluent is often called liquid nutrients, to characterize its value. It's odor has been significantly reduced at this stage and any harmful bacteria such as fecal coliforms are 95% reduced.

The volume of liquid nutrients is significant, about 90% of the initial input manure volume. Waste storage facilities are required to store the treated liquid, so it can be applied as fertilizer to cropland as weather permits.

The size of the storage facility must be adequate to meet farm requirements during the non-growing season. Many farms use earthen lagoons to store the liquids. These lagoons are similar in size and construction to traditional livestock waste lagoons. Above ground metal storage tanks, similar to short silos, are also marketed as a storage option. These tanks may be easier to pump from, and they offer a solution in cases where there is not enough space available for an earthen lagoon.

Those farms that can be equipped with larger storage facilities which have longer storage periods, allow flexibility in managing the waste to acommodate weather changes, equipment availability or breakdown, and overall operation management.