- Alteration of Terrain Bureau
- Beach Inspection Program
- Best Management Practices to Prevent Groundwater Contamination
- Biomonitoring Program
- Boat Pumpouts (Clean Vessel Act) Program
- Coastal Program
- Chemical Monitoring Waivers
- Dam Removal & River Restoration Program
- Dam Bureau
- Drinking Water and Groundwater Bureau
- Drinking Water Source Protection Program
- Drought Management Program
- Emergency Action Plans Program
- Engineer Prequalification
- Exotic Species Program
- Groundwater Discharge Permitting and Registration
- Groundwater Reclassification
- Instream Flow Protection Pilot Program
- Interactive Lakes Ecology Curriculum
- Lakes Management and Protection Program
- Land Resources Management
- Large Groundwater Withdrawal Permitting Program
- Lead and Copper in Drinking Water
- New Community Well Sitings
- New Hampshire Environmental Laboratory Accreditation Program
- Small Water System Help Center/Capacity Assurance
- Nonpoint Source Pollution Program
- Permitting of Sources of Bottled Water
- Private Well Testing Program
- Project WET
- Public Pool and Spa Program
- Public Waters/Great Ponds Program
- Regional Environmental Planning Program
- Rivers Management & Protection Program
- Shellfish Program
- Shoreland Program
- Stormwater Program
- Subsurface Systems Bureau
- Surface Water Quality Assessment Program – Section 305(b) / 303(d)
- Total Maximum Daily Load (TMDL) Program
- Volunteer Lake Assessment Program
- Volunteer River Assessment Program
- Wastewater Engineering Bureau
- Water Conservation
- Water Quality Certification Program
- Water Quality Standard Advisory Committee
- Water Resources Plan Process
- Water Supply Land Conservation Grants
- Water System Emergency Planning/Security
- Water Use Registration and Reporting Program
- Water Well Board
- Water Works Operator Certification Program
- Watershed Assistance Section
- Watershed Management Bureau
- Wetlands Bureau
- Winnipesaukee River Basin Program
- Youth Recreation Camp Licensing Program
Programs, Bureaus and Units