Rivers in Shajapur district include the Chambal River, Parbati River, the Kali Sindh River, etc. The entire district of Shajapur lies in the drainage area of the Chambal, which is a major tributary of the Yamuna River. The Chambal River itself flows towards the north beyond the western boundary of the Shajapur district in the state of Madhya Pradesh in central India. Its tributaries flowing in the district are the Parbati, the Newaj, the Kali Sindh, the Lakhundar, the Ahu, the Au, and the Chhoti Kali Sindh.
The Parbati River or the western Parbati rises from the Northern slopes of the Vindhya Mountain Range near Siddiqueganj in the Sehore district. This river flows towards the north-east and drains a narrow belt in the eastern portion of the Shajapur district. It also forms the eastern boundary which is common with Sehore district. The river flows further in the Rajgarh district and Guna district of Madhya Pradesh and Kota district of Rajasthan. Below Narsinghgarh, the river attains a large size. The Parbati River joins the right bank of the Chambal River at Palighat after a course of three hundred and fifty four kilometres of which about fifty kilometres within or along the boundary of the district.
The Newaj tributary of the Parbati River rises near the western boundary of Sehore district. It flow towards the north and enters the district of Shajapur near Geglekheri. This river drains most of the parts of Shujalpur tehsil. After a course about forty eight kilometers in the district the river passes in to the Rajgarh district and ultimately joins the Chambal River.
The Kali Sindh River rises from the Vindhyan hill in the Dewas district. This river flows to the north, traversing across Shajapur tehsil. It leaves the district above Sarangpur but after flowing for about nine kilometers it retouches the north-eastern boundary of the Shajapur district which is common with the district of Rajgarh. Before it leaves the district finally, the Lakhundar meets it on the left bank. Sundarsi, Kalisindh Railway Station, Sarangpur and Jhalawar are important settlements on its bank. It is an important tributary of the Chambal River. The length of this river within the district is forty kilometres and along north-eastern boundary it is fifty six kilometres.
The Lakhundar River rises from the Chandgarh hill in the Dewas district. It enters the district of Shajapur near the south-western corner and flows due north through Shajapur and Susner tehsil. It also forms the inter-district boundary with Ujjain and inter-tehsil boundary between Agar and Susner. This river joins the left bank of the Kali Sindh. Out of its length of about seventy two kilometers, about sixty four kilometers lie in the district of Shajapur.
Another river of importance in this district is the Ahu. It is a small stream, rising from Tonkra hill of Agar tehsil. It flows along the north-western boundary of the district common with Jhalawar of Rajasthan state. The Au, an eastern stream of Ahu rises near Agar and forms the inter-tehsil boundary with Susner. The Chhoti Kali Sindh rises from the vicinity of Dewas and flows to the north-west in Ujjain district, Dewas district, Shajapur district and Jhalawar district. In the district of Shajapur it flows mostly along the south-western and western boundaries. The banks are cut up and show signs of growing ravines.