This study aims to estimate chlorophyll-a concentration in rivers using multi-spectral RapidEye imagery and Spectral Mixture Analysis (SMA) and assess the applicability of SMA for multi-temporal imagery analysis. Comparison between images (acquired on Oct. and Nov., 2013) predicted and ground reference chlorophyll-a concentration showed significant performance statistically with determination coefficients of 0.49 and 0.51, respectively. Two band (Red-RE) model for the October and November 2013 RapidEye images showed low performance with coefficient of determinations ($R^2$) of 0.26 and 0.16, respectively. Also Three band (Red-RE-NIR) model showed different performance with $R^2$ of 0.016 and 0.304, respectively. SMA derived Chlorophyll-a concentrations showed relatively higher accuracy than band ratio models based values. SMA was the most appropriate method to calculate Chlorophyll-a concentration using images which were acquired on period of low Chlorophyll-a concentrations. The results of SMA for multi-temporal imagery showed low performance because of the spatio-temporal variation of each end members. This approach provides the potential of providing a cost effective method of monitoring river water quality and management using multi-spectral imagery. In addition, the calculated Chlorophyll-a concentrations using multi-spectral RapidEye imagery can be applied to water quality modeling, enhancing the predicting accuracy.