The Jajar River is the most popular river located in Betahwalang Village, Demak Regency, characterized by an estuary protruding a shallow depth leading to turbulence that occurs intensively both by natural phenomena and anthropogenic activities. As an extensive river heavily affected by human activities, various types of litter have degraded the water quality surrounding its estuary. By employing quantitative methods, this study mapped the horizontal distribution of nitrate concentration at nine stations representing areas close to the estuary, middle of the estuary, and far from the estuary using MIKE 21 Flow Model and ArcMap v.10.8. Later, the significant correlation between nitrate concentration and water depth was processed using SPSS v.24. The results showed that the nitrate concentration at nine stations ranged from 2.3-5.3mg/L with an average of 3.055mg/L has exceeded the threshold following the Decree of the State Minister of the Environment Number 51 of 2004 regarding Standard Quality of Seawater. Nitrate concentration and depth at all stations did not show a significant correlation (r= -0.651, p>0.058). However, when the depth was divided into two categories (<1m and 1m), a significant negative correlation was found (r = -0.896, p<0.040, and r = -0.913, p<0.045), emphasizing that the deeper the waters, the lower nitrate they contained