Fruit juices are the beverages having nutritious value playing an important role in healthy diet because of its natural composition which gives different types of nutrients. Pectinases are enzymes which are widely used for fruit juice processing and clarification. Since, ground water is getting contaminated in all areas due to industrial, cosmopolitan, agricultural activities. The drinking water has to be treated to remove the microbes and inorganic chemicals. Since, enzymes were used for the fruit juice processing the microbes and chemical constituents will definitely affect the enzyme and clarification process. This work mainly emphasis on the pre- treatment of water samples which are to be utilized for fruit juice processing.Atomic Absorption spectrophotometer (AAS) was utilized to determine analytes which are dissolved in aqueous samples after acceptable filteration, evaporation and acid preservation. The analytes measured in water sample includes Lead, Manganese, Copper, Zinc, Iron. The results showed that microorganisms and chemical constituents were removed up to an acceptable limit. This pre-treated water samples can be utilized for the juice processing process.