Algal blooms not only destroy fish habitats but also diminish biological diversity of ecosystem which results into water quality deterioration of 4 major rivers in South Korea. The relationship between algal bloom and environmental factors had been analyzed through the cross-correlation function between concentration of chlorophyll a and other environmental factors. However, time series of cross-correlations can be affected by the stochastic structure such auto-correlated feature of other controllers. In order to remove external effect in the correlation analysis, the pre-whitening procedure was implemented into the cross correlation analysis. The modeling process is consisted of a series of procedure (e.g., model identification, parameter estimation, and diagnostic checking of selected models). This study provides the exclusive correlation relationship between algae concentration and other environmental factors. The difference between the conventional correlation using raw data and that of pre-whitened series was discussed. The process implemented in this paper is useful not only to identify exclusive environmental variables to model Chl-a concentration but also in further extensive application to configure causality in the environment.