As the optimal linear filter and estimator, the Kalman filter has been extensively utilized for state estimation and prediction in the realm of lumped parameter systems. However, the dynamics of complex industrial systems often vary in both spatial and temporal domains, which take the forms of partial differential equations (PDEs) and/or delay equations. State estimation for these systems is quite challenging due to the mathematical complexity. This work addresses discrete-time Kalman filter design and realization for linear distributed parameter systems. In particular, the structural- and energy-preserving Crank−Nicolson framework is applied for model time discretization without spatial approximation or model order reduction. In order to ensure the time instance consistency in Kalman filter design, a new discrete model configuration is derived. To verify the feasibility of the proposed design, two widely-used PDEs models are considered, i.e., a pipeline hydraulic model and a 1D boundary damped wave equation.