Quick measurement of heavy metal contents in water is important for monitoring the abrupt environmental pollution. A method for quick measurement of Pb and Cd contents in water using a portable instrument which is based on bio-enzyme (DNAzymes) sensor technique is reported. The instrument was calibrated based on the linear relations between the recommended and measured concentrations of standard solutions using a bio-enzyme sensor. The range of measurable concentrations were 2~100 μg/L for Pb and 0.1~1.0 mg/L for Cd. Heavy metals can be conveniently measured in the field within 3~5 min. Because the uses of DNAzymes can quickly obtain the contents of trace metals in polluted waters, it is promising in the instantaneous monitor of heavy metal pollution in the field.