Anthropogenic activities on land will affect the carbon system in coastal waters. This condition will affect the role of coastal waters as a source or sink of carbon. This research will examine the distribution of carbonate systems and estimate CO2 fluxes. Water samples were taken at 30 stations as well as measuring in situ water parameters including pH, temperature, salinity, and pressure. Alkalinity was analysed based on the titration method, chl-a using the fluorometer method, and carbonate system parameters (pCO2(sea) and DIC) calculated using CO2SYS.xlsm. The pCO2(atm) value is calculated based on atmospheric data from satellite data, including the saturation vapour pressure of sea air in the atmosphere, fraction mol of CO2, and sea level pressure. Pearson correlation analysis was used to see the correlation between the measured parameters and CO2 flux. Carbon flux is determined based on the difference between atmospheric and oceanic pCO2. The DIC calculation result was in the range of 1,946.09 µmol/kg - 2,061.65 µmol/kg and the total alkalinity was 2,156.86 µmol/kg - 2,264.71 µmol/kg. Based on this value, Jepara coastal waters have pCO2(sea) of 573,800 micro-atmospheric (µatm) which is higher than pCO2(atm) (i.e., 386,772 µatm). The input of organic/inorganic carbon resulting from anthropogenic processes on land has influenced Jepara coastal waters which act as a source of CO2 into the atmosphere amounting to 103,799 mmol/m2/day. The results of this research can be used as a reference for managing coastal areas to achieve low carbon emissions.