This study introduces a more recent data analysis method, Hilbert Huang Transform method (HHT), to describe contaminant concentration data of a non-stationary and non-linear nature. In order to improve the modeling of the contaminant concentrations, it is proposed to first process the data using the Empirical mode decomposition (EMD) method from HHT to obtain a collection of intrinsic mode functions (IMFs) which can then be modeled separately using either autoregressive moving average (ARMA) models expanded with a seasonal term, or linear regression analysis, depending on the nature of the IMF. Three priority contaminants measured at Niagara-on-the-Lakes are selected for this study. It is found that the trend of fluoranthene concentrations from April of 1986 to March of 1997 is decreasing and then beginning to increase; the 1,2,4-trichlorobenzene concentrations are decreasing; while the dieldrin concentrations are decreasing. With HHT, appropriate time series models can be identified and constructed for the studied contaminant concentrations to better illustrate the variability of each IMF (and thus the contaminant concentrations) for the studied period. For all data sets modeled in this study, pre-processing the data with HHT allowed for higher R2 values, correlation coefficients and lower sum of squared errors when compared to modeling without HHT. It is thus confirmed that pre-processing the data with HHT and modeling with time series analysis will provide a more effective means of the studied data sets when identifying and analyzing the trends and variability of studied contaminant concentrations in the Niagara River.