Organization contains following Directorates and their activities are as under:

1. Environment Management (EM) Directorate:

   The directorate is responsible for, examination of environmental impact assessment reports received from the Ministry of Environment & Forests (MoEF) and offering comments/suggestions at Expert Committee (EC) meeting of MoEF for environmental clearance (Chief Engineer (EMO) is a member representing, CWC), preliminary screening of projects from environmental angle before taking it for detailed examination in CWC, conducting environmental evaluation/impact assessment study of some selected projects, assisting Chief Engineering (EMO) in his functions in the capacity of Chairman of Technical Advisory & Review Committee related to Environmental Impacts Assessment and Socio-Economic Study of Pancheshwar multipurpose project, facilitating forest clearance from MoEF, participating in Forest Advisory Committee meetings and examination of references from MoEF/MoWR for funding of environment related project proposals of NGOs. It is responsible for monitoring of implementation of environmental safeguards for river valley projects through Multidisciplinary – Inter-Ministerial National Environmental Monitoring Committee for River Valley Projects (NEMCRVP), State Environmental Monitoring Committee and Project Environmental Management Committees, organizing meetings of NEMCRVP and drafting of various standards under WRDC 23 (Assessment and Management of Environmental Impacts of River Valley Project). It is also responsible for looking after the rehabilitation and resettlement aspects for affected persons of reservoir projects, assistance in formulation of National Rehabilitation and Resettlement Policy (Ministry of Rural Development), application of guidelines for preparation of rehabilitation and resettlement action plan as well as maintenance of related database, examination of rehabilitation and resettlement aspects and action plans for multipurpose/irrigation projects referred by the States and Union Territories and on the spot assessment of resettlement sites of the reservoir projects for appraisal of implementation of R&R policies formulated by States/Project Authorities. The directorate also deals with the matters pertaining to minimum flow/environmental flow.

2. Remote Sensing Directorate:

   This directorate is responsible for application of Remote Sensing and GIS Techniques in water resources sector, collection, collation and analysis of spatial data using GIS techniques, capacity building in application of spatial data technology for water resources development and management, participation in the activities of National Natural Resources Management System (NNRMS) in relation to water resources development and management and coordination with ISRO, NRSA and other space agencies regarding application of spatial data technology, advising the state irrigation departments and MoWR in issues related to application of spatial data technology in the water resources development and management. This directorate, also act as nodal directorate for pursuing the activities of National Water Informatics Centre (NWIC) besides populating and constantly updating India-WRIS website; Integrating State WR data/State WRISs with India-WRIS, developing uniform data protocols for WRIS data so as to achieve consistency in the multi-agency data, etc.

3. Watershed and Reservoir Sedimentation Directorate:

   This is responsible for collection and compilation of sediment data of various reservoirs in the country and updating compendium prepared earlier, conducting hydro-graphic survey of important reservoirs in the country, assisting Project Authorities/State Governments in matters connected with hydro-graphic surveys, sediment control measures, sediment measurement techniques, assessment of sedimentation rates/sediment trap efficiency in Indian reservoirs for better future planning etc., coordination with Ministry of Agriculture on Soil Conservation or Enhancing Productivity of Degraded Lands in the catchments of River Valley Projects and Flood Prone rivers (RVP & FPR) under Macro Management and preparation of status report on Watershed Management and Water Harvesting. Additionally, activities of Indian National Committee of Surface Water (INCSC) will also be handled by this directorate.