Chemical reaction systems act as the basis to get the desired products from raw materials. An in-depth understanding of all the underlying rate processes is necessary for monitoring, control and optimization of chemical reaction systems. Traditional representation of a reaction system by means of the conservation equations (material and energy balances) leads to a set of highly coupled differential equations. These coupled ODEs provides overall contributions of all the underlying rate processes, and hence, it is difficult to analyse the effect of each rate process in a reaction system. In this dissertation, an alternative representation of reaction systems in terms of decoupled variables, namely, vessel extents is introduced. The advantages of using the representation in terms of the decoupled variables over the traditional representation are investigated for data reconciliation, model identification and parameter estimation, and state reconstruction and estimation.