Rivers act as a natural system of circulating CO2 among atmosphere and terrestrial, in which the increasing watershed urbanization and anthropogenic stress could affect the CO2 emission. Hence, in this chapter, the spatial and temporal variations of partial pressure of carbon dioxide (pCO2) in the Miri River of Northern Borneo was accessed, and the related hydrochemical controlling factors for the riverine pCO2 was also examined. Surface water samples were collected at various sections (upstream, mid-stream and downstream) of the river during two different seasons (monsoon and post monsoon). The collected samples were analysed for physical parameters, major ions and stable isotopes using standard procedure. The pCO2 values were computed by using the geochemical model, WATEQ4F. The results show that the high pCO2 was observed during monsoon period, with an average of 0.102. Geochemical data also supports the pCO2 variability with respect to locations and seasons. The closed system of high pCO2 in the upstream section indicate atmospheric CO2 input, which increase protons and HCO3 with the undersaturation state of calcite, favours carbon sink. Whereas, the closed system of low pCO2 in the downstream section suggests the weathering of source rocks consumed protons and or degassing of CO2 leading to saturation state of calcite, considered as carbon source. This prototype study gives the spatial and temporal variability of pCO2 in an urbanized river, and it can be used as a model to study the other tropical rivers in this region.