The irrigation department was initially a part of the Public Works Department. Based on the recommendation of The Retrenchment Committee, the staff of the Public Works Department underwent reduction and led to the formation of the Irrigation Division, with three sub-divisions and nine sections to carry out the irrigation works of the State. Later on, as per the G.O (P) No 27/90/PW & T dated 29th March 1990, the Public Works Department was bifurcated into two departments viz, Irrigation Department and Public Works Department with effect from 1st April 1990.

The Head Quarters of the Irrigation Department is located in the Public Office Complex, Thiruvananthapuram, and is under the control of the Chief Engineer, Irrigation & Administration. The Irrigation & Administration wing deals with the Major & Minor Irrigation works across the state, Flood Control & Coastal Zone Management, and Salt Water extrusion apart from the general administration of the department.