Measurements acquired from distributed physical systems are often sparse and noisy. Therefore, signal processing and system identification tools are required to mitigate noise effects and reconstruct unobserved dynamics from limited sensor data. However, this process is particularly challenging because the fundamental equations governing the dynamics are largely unavailable in practice. Reservoir Computing (RC) techniques have shown promise in efficiently simulating dynamical systems through an unstructured and efficient computation graph comprising a set of neurons with random connectivity. However, the potential of RC to operate in noisy regimes and distinguish noise from the primary dynamics of the system has not been fully explored. This paper presents a novel RC method for noise filtering and reconstructing nonlinear dynamics, offering a novel learning protocol associated with hyperparameter optimization. The performance of the RC in terms of noise intensity, noise frequency content, and drastic shifts in dynamical parameters are studied in two illustrative examples involving the nonlinear dynamics of the Lorenz attractor and adaptive exponential integrate-and-fire system (AdEx). It is shown that the denoising performance improves via truncating redundant nodes and edges of the computing reservoir, as well as properly optimizing the hyperparameters, e.g., the leakage rate, the spectral radius, the input connectivity, and the ridge regression parameter. Furthermore, the presented framework shows good generalization behavior when tested for reconstructing unseen attractors from the bifurcation diagram. Compared to the Extended Kalman Filter (EKF), the presented RC framework yields competitive accuracy at low signal-to-noise ratios (SNRs) and high-frequency ranges.