The Department is headed by the Principal Secretary as Administrative Head at the Government level and by a Chief Engineer at the Directorate level with 3 (three) Circles, 14 (fourteen) Divisions and 42 (forty two) Sub Divisions. The Department has a total of 1610 Regular Employees and 1407 Work Charged Employees as on January 2021 to carry out various Departmental schemes.

The Department has a centrally sponsored Water and Sanitation Support Organization (WSSO) headed by Chief Engineer, Sanitation & WSSO, which looks after Swachh Bharat Mission (Grameen), Support Activities and Water Quality Monitoring & Surveillance (WQMS) of the Jal Jeevan Mission (JJM).