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 constructed a scintillator based underwater muon detection system which can measure average water column density by counting surviving muons at the bottom. The detector system deployed in the North-Eastern Mediterranean at METU-IMS Harbour in Mersin/Turkey. Initial observations show consistent muon flux measurements with previous studies. In this work validation of muon detection was made for Mixed Layer Depth measurements. In order to calibrate the MLD estimation via muon count, water density measurements with CTD (Conductivity, Temperature, Depth) will be done simultaneously. In this work we will present our first measurements of atmospheric muon flux together with a simple approach to distinguish muons from other particles. This work is actualization of a previous study "Mixed Layer Depth Measurement in Coastal Waters Utilizing Atmospheric Muons" (10.1175/JTECH-D-24-0044.1) published in Journal of Atmospheric and Oceanic Technology.