The influence of sample matrix composition on the infrared sensing response to chlorinated hydrocarbons was investigated. The parameters of chemical oxygen demand (COD) and total organic carbon (TOC) were used to characterize water samples from natural and industrial waters. Chlorobenzene was selected as a model target for assessing the effect of the sample matrix, defined by their COD and TOC values, on the infrared optical measurements. It was found that it was possible to directly compare recovery values with TOC and COD values at low concentrations of the latter. However, where TOC and COD values were high, in particular for industrial waters, the influence of sorbing natural organic matter was low compared to the total organic carbon due to the synthetic component of the water. Therefore, when measuring natural environmental waters, it was possible to use COD and TOC values to obtain the true concentration of the analyte in the sample, but for industrial samples, the COD and TOC values were not good indicators.