The use of natural coagulant protein in drinking water treatment has been discussed for a long time, though the method is still not in practice, probably due to limited knowledge and availability of material. In the present work, different Mustard varieties were tested for the presence of coagulant protein compared with Moringa seed extract and their potential application in water treatment. The coagulation activity of the protein extract was measured using synthetic clay solution as well as water from pond. The protein content was determined by Bradford method, molecular mass determined by Sodium dodecyl sulfate–polyacrylamide gel electrophoresis, and peptide sequence was analyzed by Mass spectrometry. Extract of Mustard (large) and Moringa seed showed coagulation activity of ≅70 and ≅85 % after 90 min, respectively. Interestingly, seed extracts from other Mustard varieties had coagulation activity after heat activation at 95 °C for 5 h. However, the coagulation activity of Mustard seed extract against turbid pond water was higher (≅60 %) compared to Moringa seed extract (≅50 %). The peptide sequence analysis of 6.5 and 9 kDa proteins was found to be homologous to Moringa coagulant protein and napin3, respectively. To our knowledge, this could be the first report on Mustard seed having coagulant protein. The coagulation activity of Mustard (large) against highly turbid pond water suggested that it could be a potential natural coagulant for water treatment.