Abstract: The seasonal fluctuations in various physico-chemical parameters in the water were investigated in the six sampling sites namely Neyyar Dam, Kallikkadu, Mandapathinkadavu, Aruvippuram, Neyyattinkara and Poovar of Neyyar River on the basis of their physiographic distribution during north east monsoon and pre-monsoon. Water temperature broadly fluctuated between 27.00C at Neyyar dam in north east monsoon to 33.20C at Neyyattinkara in pre-monsoon. Though, seasonal influence was marginal, a lowering in pH was generally visible during north east monsoon. In the station near coast, impact of saline intrusion was obvious in the distribution of EC. TDS varied broadly between 20.4mg/l to 16000mg/l, respectively in the reservoir and the Poovar. Correspondingly the chloride also has been gradually increasing towards downstream. In general turbidity is found to be low except occasional high values at Kallikadu. Our study indicates that alkalinity values are very less all along the river during both seasons and total hardness exceeds the prescribed limits in downstream stretches. The samples in the midland and lowland invariably showed considerable concentrations of the nutrient. Inverse to the distribution of DO, the BOD value was the minimum at reservoir and the maximum at Poovar. Significant correlations between the parameters were observed by using SPSS software.