The perineal River Musi is flowing from centre of the state capital city and bifurcating in to twin cities Hyderabad and Secunderabad. Every day the River Musi is carrying loads of domestic and industrial waste (effluents) along with water. The groundwater quality is assessed by determining the content of heavy metals like Al, As, Ba, Co, Cr, Cu, Zn, Pb, Ni and Mn. The life sustainability of the ecological system is dependent on the concentration of these heavy metals, which is life threatening when they are above their standard permissible limits. The discharge from industrial effluents and domestic waste along the Musi River are the main source of heavy metals in groundwater. Added to this the slow movement of surface water in the river accumulates and precipitates the heavy metals. The adverse impacts on local water bodies and shallow aquifers on untreated and or partially treated waste water used for irrigation have been significantly observed. This effect is observed in the vicinity of Musi River making the ground water unsuitable for domestic or agricultural purposes. Hence, there is an urgent need to find the solution to this problem with a suitable plan and an achievable strategy. Bio-remediation in the surface water bodies could check the depletion and contamination of aquifers for sustainable use. This can be achieved with an experimental strategy of excessive plantation along the river banks.