The analysis of covariance model (ANCOVA) with heterogeneous variance first-order autoregressive error covariance structure (ARH1) was used to model the differences in fecal streptococci concentration in Iloilo River over time with fixed site and seasonal effects as primary factors of interest, and water temperature, pH, dissolved oxygen, and salinity as covariates. The restricted maximum likelihood estimation (REML) procedure was used to derive the parameter estimates and the Kenward-Roger adjustment in the degrees of freedom was used to better approximate the distributions of the test statistics. The effect of season was highly significant (p = 0.0019). The site effect was significant at the 0.0539 level. The effects of water surface temperature and pH were significant at the 0.0655 and 0.0828 level, respectively. The effects of dissolved oxygen and salinity were not significant. Although the coefficient of determination was modest, the result of the study is useful in characterizing the dynamics of Iloilo River bacteriological system which contributes to an improved understanding of the Iloilo River water quality.