A study was made of the chaetognaths of the Cochin Backwater. Krohnitta pacifica Aida, Sagitta bedoti Beraneck, Sagitta enflata Grassi and S. Oceania Gray were the species found in the collections. S. bedoti was the dominant chaetognath. S. Oceania is recorded for the firstt ime from Indian waters. Representatives of different sizes of S. bedoti belonging to two maturity cycles were encountered in a few samples. This phenomenon of recurring maturity stages in S.bedoti is observed for the first time and this may ensure sufficient reproductive potential to maintain the population in an estuarine habitat. Occurrence of S. enflata in great abundance at barmouth during the post-monsoon period is associated with the incursion of oceanic water into the area. Salinity plays a major part in controlling the distribution of chaetognaths in this estuary. They penetrated to the southernmost part of the estuary during the pre-monsoon period when a uniform high salinity prevailed throughout the system. In the post-monsoon period the chaetognath population synchromically followed the steep gradient in salinity along the estuary and became restricted to its seaward end. It is suggested that during the monsoon period they are removed from, the area and fresh recruits from the sea are brought back to the system along with the incoming waters of the post-monsoon period.