Pollution in Pekalongan waters is one of the environmental problems caused by the industrial city. Batik industry, the most common activity at Pekalongan, uses a lot of water and generates a lot of effluent because it involves an aqueous process when dyeing fabric. This wastewater, contains heavy metal contaminants like hexavalent chromium (Cr+6), copper (Cu), and lead (Pb), generally finds its way to rivers that run across Pekalongan. The contamination level, spatial distribution, and transport simulation of copper (Cu) and chromium (Cr) in water were investigated in the Loji and Banger rivers in Pekalongan, Indonesia. A two‐dimensional hydrodynamic model was constructed to simulate heavy metal concentrations in marine environment of Pekalongan City, Indonesia. The model's kinetic processes comprised air exchange, transportation, and deposition. Thus, Cu concentrations were below Indonesia's threshold, but Cr, especially in the river and outlet river, exceeded it. Both rivers have 0.002 mg/L Cu. Since water freely flows at Banger River Estuary, Cr concentration reach the highest in both rivers, 0.1056 mg/L. The evaluation findings and the numerical Cu and Cr calculation model created in this work have important research ramifications for preventing and controlling heavy metal pollution.