All individual NPDES permits include a certain set of basic elements.

The first is perhaps the most obvious -- a specific, numeric, measurable set of limits on the amount of various pollutants that can appear in the wastewater discharged by the facility into the nation's waters. Such limits are often expressed as concentrations, combined with allowed volumes of discharge. Or, limits can be expressed as mass discharged per unit time (day, week, and so forth). Limits must be expressed in such a way that they cannot be met simply by diluting the facility's effluents with clean water just before they are released into the receiving water.

As explained in more detail later, such limits can be either technology based or water quality based. Regardless of how they are derived, effluent limits are performance standards; a permittee is free to use any combination of process modification, recycling, end-of-pipe treatment, or other strategies to meet them.

NPDES permits can also require the use of certain structural or non-structural BMPs. For "traditional" point sources, municipal wastewater plants and industrial facilities, BMPs are supplemental to end-of-pipe performance standards. For wet weather-related point sources, such as combined sewer overflows (CSOs) and municipal and industrial storm water runoff, BMPs are often the only "control" requirements in the permit.

If meeting the effluent limits in a permit will require upgrading in-plant or wastewater treatment processes, it would not be reasonable to require compliance with such limits upon issuance of the permit (in the case of existing sources). Hence, permits for such sources can include a compliance schedule. Such schedules usually include not only a final date upon which effluent limits must be met but also interim milestones, such as dates for onset of needed construction. EPA guidance specifies that compliance schedules extend no longer than the term of the permit.

Most individual NPDES permits include detailed monitoring requirements that specify what pollutants the permittee must monitor for in their discharge, how frequently the monitoring should be done, and what sampling and analytic techniques should be used. (Though EPA and states conduct some inspections and compliance monitoring, the vast majority of data about the contents of the discharges from NPDES facilities are collected by the permittees themselves.) In the past, permits required only monitoring of the facility's discharges, but in recent years, some states have required some facilities to sample and analyze the waters into which they discharge as well.

If a permit contains monitoring requirements, it will also include reporting requirements. Permittees are required to regularly submit the results of the monitoring required in their permit. Most commonly these Discharge Monitoring Reports must be submitted monthly, but in some cases they are less frequent. (General permits often require few, if any, monitoring or reporting requirements.)

All NPDES permits include a standard set of clauses, including provisions for reopening the permit if new information or other specific circumstances justify possible changes, authority to revoke the permit for cause, and authority for the permitting authority to enter the facility and perform inspections.

An NPDES permit also includes a cover page (permitting authority, permittee, statutory and regulatory authorities, and effective/expiration dates), special conditions (e.g., studies, compliance schedules), and standard conditions (boiler plate language included in all permits). Along with a draft permit, the regulatory authority must include an explanation of how the discharge limits were derived.