In southern part of India, most of the precipitation occurs due to south-west monsoon during the months of June to September. Storage reservoirs are constructed to store the run-off volume and utilize it for long term requirements in the command such as irrigation, power generation, domestic water supply etc. The sediment deposition in the reservoir is a continuous and complex process. Sediment in a river which originates from the land erosion process in the catchment is propagated along with the river flow and finally gets deposited in the reservoir. This has adverse effect such as reduction in storage capacity and increase in backwater levels. For the long term and yearly planning of efficient utilization of reservoir capacity, estimation of sediment deposit is not only sufficient but also estimation of trapped sediment at different levels in the reservoir is required. Differential Global Positioning System (DGPS) based Integrated Bathymetric Survey System for hydrographic survey is used for estimation of sediment deposition pattern in the Koyna reservoir. In this method three or more satellite based GPS receivers are used in differential mode for positioning. Ecosounder is used for depth measurements. GPS reference receiver is located at a known latitude and longitude position and GPS mobile receiver is located on the survey boat. Both the GPS operate in differential mode through a communication link. From this study (2004) it is observed that sedimentation rate in Koyna reservoir is more than 6.5 Ham/100 sq.km/year anticipated in 1949.