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USDA's Natural Resource Conservation Service (NRCS)
http://www.hi.nrcs.usda.gov/

US EPA: Coastal Nonpoint Source Pollution Control Program
http://www.epa.gov/OWOW/NPS/coastnps.html
US EPA: Total Maximum Daily Loads Program
http://www.epa.gov/owowwtr1/tmdl/
U.S. Geological Survey: National Water Quality Assessment Program
http://water.usgs.gov/nawqa/index.html
U.S. Geological Survey: Water Resource Data for Hawaii and the Pacific
http://hi.water.usgs.gov/
U.S. Army Corps of Engineers-Honolulu District
http://www.poh.usace.army.mil/index.asp
 
Rules and Regulations/Permits
U.S. Army Corps of Engineers-Honolulu District
http://www.poh.usace.army.mil/regulatory.asp
 
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In the news
On January 2nd, USDA proposed rules governing the Conservation Security Program (FR vol 69, No. 1, page 194). CSP, run by NRCS, is to provide financial/technical assistance to agricultural producers who conserve and improve the quality of soil, water, air, etc. in "priority watersheds". NRCS will nationally prioritize watersheds based on a score derived from a composite index of existing natural resource, environmental quality and agricultural activity data. Soil quality and water quality, as described in Section III of the NRCS Field Office Technical Guide are nationally significant resource concerns. The watershed prioritization will consider several factors, including but not limited to, vulnerability to surface and groundwater quality.