Scroll Top
Aquaculture Hub circular logo

National Pollutant Discharge Elimination System (NPDES) Permit

A. Legal Authority

  • Clean Water Act, as amended, 33 U.S.C. 1342
  • Title 40 CFR, § 122.
  • Chapter 342D, Part III, HRS, Water Pollution Control
  • Title 11, Chapter 54, HAR, Department Of Health, Water Quality Standards
  • Title 11, Chapter 55, HAR, Department Of Health, Water Pollution Control


B. Purpose

The purpose of the National Pollutant Discharge Elimination System (NPDES) permit is to protect the water quality of the U.S., and this case Hawaiʻi, by regulating the discharge of wastewater from fixed point sources into surface waters, including wetlands and coastal waters. Fixed point sources include pipes, ditches, channels, tunnels, wells, etc., from which pollutants may be discharged. Ponds, tanks, cages or other similar aquaculture infrastructure are generally considered fixed point sources for purposes of law.

There are two levels of permits, a general permit and an individual permit. The activities that qualify for a general permit are adopted by rules (Chapter 11-55, HAR). They include discharges that are similar in nature, minor and non-controversial. The activities that must seek an individual permit do not qualify for a general permit and are site specific in their potential impacts.

C. Applicability to Aquaculture

The NPDES permit applies to several types of aquaculture systems, generally categorized under the terms; Aquaculture Project and Concentrated Aquatic Animal Production Facility (CAAP). “Aquaculture Project” means a defined managed water area which uses discharges of pollutants into a designated area for the maintenance or production of harvestable freshwater, estuarine, or marine plants or animals. “Designated” means the portions of waters of the U.S. within which the applicant plans to confine the cultivated species, using a method of plan or operation (including, but not limited to, physical confinement) which, on the basis of reliable scientific evidence, is expected to ensure the specific individual organisms comprising an aquaculture crop will enjoy increased growth attributable to the discharge of pollutants and be harvested within a defined geographic area.

“Concentrated Aquatic Animal Production Facility” means a hatchery, fish farm, or other facility which contains, grows or holds aquatic animals in either of the following categories, or which the director of the Department of Health (DOH) designates as such on a case-by-case basis:

  • Cold water fish species or other cold water aquatic animals including, but not limited to, trout and salmon in ponds, raceways, or other similar structures which discharge at least 30 days per year but does not include:
    • Facilities which produce less than 20,000 pounds of aquatic animals per year; and
    • Facilities which feed less than 5,000 pounds of food during the calendar month of maximum feeding.
  • Warm water fish species or other warm water aquatic animals including, but not limited to, catfish, sunfish, and minnows in ponds, raceways or other similar structures which discharge at least 30 days per year, but does not include:
    • Closed ponds which discharge only during periods of excess runoff; or
    • Facilities which produce less than 100,000 pounds of aquatic animals per year.

The NPDES permit sets specific limits on discharge volume and effluent concentration. It is issued for a set time period of no more than five years and is renewable and transferable. Once granted, monitoring of effluent volume and concentration is usually required. Title 11, Chapters 54 and 55 of the DOH Administrative Rules should be reviewed for specific requirements for any site.

D. Administering Agency

The Department of Health, Clean Water Branch (CWB) is responsible for administering the NPDES permit requirements.

Clean Water Branch
Environmental Management Division
Department of Health
State of Hawaiʻi
919 Ala Moana Blvd., Room 301
Honolulu, Hawaiʻi 96814-4920
Phone: 808-586-4309
Fax: 808-586-4352
Web site: (see web site for Neighbor Island Branch Office information: Kauai; Maui; Hilo, Hawaiʻi; and Kona, Hawaiʻi.)

E. Information Requirements

The CWB has an extensive web site that can be accessed through the link above that provides information on administrative procedures and forms needed to obtain an NPDES permit and a Zone of Mixing permit. This site also lists the Standard NPDES Permit Conditions which are attached to all approved NPDES permits. In addition, highly useful water quality maps, i.e., island maps of receiving water classifications published by the DOH Office of Environmental Planning can be found on the web site.

In general, a project application must describe the proposed activity, including location, species and number of animals, daily flow of effluent, and infrastructure making up the facility. The physical-chemical nature of the effluent, including pH, temperature, dissolved oxygen, nitrogen, and phosphorus, must be characterized. Further, it describes the receiving water and water source and the total pounds of food being fed during the calendar month of maximum feeding. Tests on the existing quality of the receiving water, a survey of the receiving water’s ecosystem and an analysis of the prevailing water currents may also be required.

Preparation of environmental review documents is not specifically required by the state. However, if the discharge of effluent or the placement of outfall structures fall under the permit authority of a federal or state agency and the project involves the potential for a significant effect on the environment, an Environmental Assessment and possibly an Environmental Impact Statement will be required. The applicant should consider, if an EA or EIS is prepared for another project permit, asking CWB if they should submit a copy to support the NPDES application.

F. Public Participation

There is no required public hearing. The Department of Health must notify the public through the Office of Environmental Quality Control (OEQC) Environmental Notice publication of their intent to issue a permit. A public hearing may be required if requested by a member of the public.

G. Process Time

The processing time for an NPDES permit varies with the complexity of the project. For minor project proposals, processing of the NPDES permit can be expected to take from three to four months from the acceptance of a completed application. Projects requiring an Environmental Assessment or Impact Statement may take considerably longer. NPDES permits are issued for a finite period of time, generally five years. All NPDES permit applications will be reviewed by the U.S. Environmental Protection Agency, Region 9 Office. Permits are renewable.

H. Sequence of Filing

There is no specific sequencing requirement for NPDES permits. Generally, for warm water aquaculture projects, an approved NPDES permit must be in place before production reaches 100,000 pounds a year or biomass at a site reaches 100,000 pounds.

I. Costs

The filing fee for an NPDES permit application for a CAAP or an Aquaculture Project is $1000. Public notice and hearing fees will vary. The cost of preparing the permit application and required information varies with the scope and complexity of the project and the nature of the surrounding environment. NPDES permits are conditioned upon the applicant conducting periodic monitoring tests during the life of the permit to ensure compliance. The costs of conducting such monitoring, including equipment and laboratory analysis, can be significant.

Blue pattern containing two shades of blue with some razor-like detail

Department of Agriculture – Aquaculture and Livestock Services
99-941 Halawa Valley Street
Aiea, Hawaiʻi 96701-5602
Phone: 808-483-7130
Fax: 808-483-7110
Web site:


Pacific Region Aquaculture and Coastal Resource Hub
2525 Correa Road, HIG 238
Honolulu, HI 96822
Phone: (808) 956-7031

Center of Excellence Sidebar Pattern

Each pattern represents a Center of Excellence. Learn more about the cultural connections and meanings behind them.