Health monitoring and prognosis of nonlinear systems is mainly concerned with system health tracking and its evolution prediction to future time horizons. Estimation and prediction schemes constitute as principal components of any health monitoring framework. In this thesis, the main focus is on development of novel health monitoring techniques for nonlinear dynamical systems by utilizing model-based and hybrid prognosis and health monitoring approaches. First, given the fact that particle filters (PF) are known as a powerful tool for performing state and parameter estimation of nonlinear dynamical systems, a novel dual estimation methodology is developed for both time-varying parameters and states of a nonlinear stochastic system based on the prediction error (PE) concept and the particle filtering scheme. Estimation of system parameters along with the states generate an updated model that can be used for a long-term prediction problem. Next, an improved particle filtering-based methodology is developed to address the prediction step within the developed health monitoring framework. In this method, an observation forecasting scheme is developed to extend the system observation profiles (as time-series) to future time horizons. Particles are then propagated to future time instants according to a resampling algorithm in the prediction step. The uncertainty in the long-term prediction of the system states and parameters are managed by utilizing dynamic linear models (DLM) for development of an observation forecasting scheme. A novel hybrid architecture is then proposed to develop prognosis and health monitoring methodologies for nonlinear systems by integration of model-based and computationally intelligent-based techniques. Our proposed hybrid health monitoring methodology is constructed based on a framework that is not dependent on the structure of the neural network model utilized in the implementation of the observation forecasting scheme. Moreover, changing the neural network model structure in this framework does not significantly affect the prediction accuracy of the entire health prediction algorithm. Finally, a method for formulation of health monitoring problems of dynamical systems through a two-time scale decomposition is introduced. For this methodology the system dynamical equations as well as the affected damage model, are investigated in the two-time scale system health estimation and prediction steps. A two-time scale filtering approach is developed based on the ensemble Kalman filtering (EnKF) methodology by taking advantage of the model reduction concept. The performance of the proposed two-time scale ensemble Kalman filters is shown to be more accurate and less computationally intensive as compared to the well-known particle filtering approach for this class of nonlinear systems. All of our developed methods have been applied for health monitoring and prognosis of a gas turbine engine when it is affected by various degradation damages. Extensive comparative studies are also conducted to validate and demonstrate the advantages and capabilities of our proposed frameworks and methodologies.