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Massive mangrove conversion into intensive pond farming has become environmental problem in Kemujan Island and Karimunjawa Island which affect the water quality. This research aimed to examine the dispersion of DO and BOD related to the current pattern in the seas west of Kemujan Island and Karimunjawa Island by using two-dimensional modelling simulations. Quantitative and descriptive methods were used to provide interpretation and analysis of the modelling simulation results. Modelling simulations were conducted in September 2019. The validation results show that the model and the field measurements has a very good. The results show that the current characteristics are dominated by tidal current, which moves westward with an average magnitude of 0.078 m/s. Furthermore, divergence, convergence and turbulence are also identified. Based on the simulation results, the prediction of DO and BOD concentrations fluctuate in Lagoon Mrican. During spring tide, the DO concentration changes from 7.95 - 8.1 mg/L into 8.55 - >9.45 mg/L and during neap tide, it changes from 8.55 - 8.7 mg/L into 9.15 - >9.45 mg/L. On the other hand, the BOD concentration increases from 0 - 0.08 mg/L to 0.88 - 0.96 mg/L during spring tide and neap tide.