After atmospheric muons enter the sea, a decreased muon count is observed at the bottom of water. Muon count is inversely proportional to the density of water which can be measured by counting muons at the bottom. Mixed Layer (ML) in Oceans is defined as the less dense upper region of the water column where turbulent mixing occurs. Mixed Layer Depth (MLD) is the depth of this region and shows diurnal, seasonal fluctuations, and spatial variations. MLD can be estimated by combining bottom muon count measurement with the sea surface temperature, salinity, and altimetry data from earth observing satellites. We proposed a scintillator based underwater muon detection system which can measure average water column density by counting surviving muons at the bottom. Using a Geant4 model, it is shown that combining this density measurement with data from Earth observing satellites enables us to continuously estimate daily mean MLD with an accuracy of 3% for down to 100𝑚 depth.