Ensemble-based methods have gained widespread popularity in the field of data assimilation. An ensemble of model realizations encapsulates information about the error correlations driven by the physics and the dynamics of the numerical model. This information can be used to obtain improved estimates of the state of non-linear dynamical systems such as the atmosphere and/or the ocean. This work develops efficient ensemble-based methods for data assimilation. A major bottleneck in ensemble Kalman filter (EnKF) implementations is the solution of a linear system at each analysis step. To alleviate it an EnKF implementation based on an iterative Sherman Morrison formula is proposed. The rank deficiency of the ensemble covariance matrix is exploited in order to efficiently compute the analysis increments during the assimilation process. The computational effort of the proposed method is comparable to those of the best EnKF implementations found in the current literature. The stability analysis of the new algorithm is theoretically proven based on the positiveness of the data error covariance matrix. In order to improve the background error covariance matrices in ensemble-based data assimilation we explore the use of shrinkage covariance matrix estimators from ensembles. The resulting filter has attractive features in terms of both memory usage and computational complexity. Numerical results show that it performs better that traditional EnKF formulations. In geophysical applications the correlations between errors corresponding to distant model components decreases rapidly with the distance. We propose a new and efficient implementation of the EnKF based on a modified Cholesky decomposition for inverse covariance matrix estimation. This approach exploits the conditional independence of background errors between distant model components with regard to a predefined radius of influence. Consequently, sparse estimators of the inverse background error covariance matrix can be obtained. This implies huge memory savings during the assimilation process under realistic weather forecast scenarios. Rigorous error bounds for the resulting estimator in the context of data assimilation are theoretically proved. The conclusion is that the resulting estimator converges to the true inverse background error covariance matrix when the ensemble size is of the order of the logarithm of the number of model components. We explore high-performance implementations of the proposed EnKF algorithms. When the observational operator can be locally approximated for different regions of the domain, efficient parallel implementations of the EnKF formulations presented in this dissertation can be obtained. The parallel computation of the analysis increments is performed making use of domain decomposition. Local analysis increments are computed on (possibly) different processors. Once all local analysis increments have been computed they are mapped back onto the global domain to recover the global analysis. Tests performed with an atmospheric general circulation model at a T-63 resolution, and varying the number of processors from 96 to 2,048, reveal that the assimilation time can be decreased multiple fold for all the proposed EnKF formulations.Ensemble-based methods can be used to reformulate strong constraint four dimensional variational data assimilation such as to avoid the construction of adjoint models, which can be complicated for operational models. We propose a trust region approach based on ensembles in which the analysis increments are computed onto the space of an ensemble of snapshots. The quality of the resulting increments in the ensemble space is compared against the gains in the full space. Decisions on whether accept or reject solutions rely on trust region updating formulas. Results based on a atmospheric general circulation model with a T-42 resolution reveal that this methodology can improve the analysis accuracy. / Ph. D.