A water treatment plant controlling method including: determining whether or not there is a correlation, in water to be treated, between a water quality index and a concentration of a pollution component having no causal relationship with the water quality index, from a result of sample analysis of the water to be treated performed periodically; and (a) under a condition that there is a correlation, statistically analyzing a distribution of measurement values of the water quality index in a previous certain period of the water to be treated, and based on a result of the statistical analysis and the correlation, estimating the concentration of the pollution component of the water to be treated; and determining an operating condition of a water treatment plant for treating the water to be treated, based on the estimated concentration of the pollution component of the water to be treated; or (b) on a condition that a correlation is absent, statistically analyzing a distribution of concentration of the pollution component in all past sample analyses of the water to be treated, and based on a result of the statistical analysis, estimating the concentration of the pollution component of the water to be treated.