The overall goals of this dissertation are to advance the field of chemical data assimilation, and to develop efficient computational tools that allow the atmospheric science community benefit from state of the art assimilation methodologies. Data assimilation is the procedure to combine data from observations with model predictions to obtain a more accurate representation of the state of the atmosphere. As models become more complex, determining the relationships between pollutants and their sources and sinks becomes computationally more challenging. The construction of an adjoint model ( capable of efficiently computing sensitivities of a few model outputs with respect to many input parameters ) is a difficult, labor intensive, and error prone task. This work develops adjoint systems for two of the most widely used chemical transport models: Harvard's GEOS-Chem global model and for Environmental Protection Agency's regional CMAQ regional air quality model. Both GEOS-Chem and CMAQ adjoint models are now used by the atmospheric science community to perform sensitivity analysis and data assimilation studies. Despite the continuous increase in capabilities, models remain imperfect and models alone cannot provide accurate long term forecasts. Observations of the atmospheric composition are now routinely taken from sondes, ground stations, aircraft, and satellites, etc. This work develops three and four dimensional variational data assimilation capabilities for GEOS-Chem and CMAQ which allow to estimate chemical states that best fit the observed reality. Most data assimilation systems to date use diagonal approximations of the background covariance matrix which ignore error correlations and may lead to inaccurate estimates. This dissertation develops computationally efficient representations of covariance matrices that allow to capture spatial error correlations in data assimilation. Not all observations used in data assimilation are of equal importance. Erroneous and redundant observations not only affect the quality of an estimate but also add unnecessary computational expense to the assimilation system. This work proposes techniques to quantify the information content of observations used in assimilation; information-theoretic metrics are used. The four dimensional variational approach to data assimilation provides accurate estimates but requires an adjoint construction, and uses considerable computational resources. This work studies versions of the four dimensional variational methods (Quasi 4D-Var) that use approximate gradients and are less expensive to develop and run. Variational and Kalman filter approaches are both used in data assimilation, but their relative merits and disadvantages in the context of chemical data assimilation have not been assessed. This work provides a careful comparison on a chemical assimilation problem with real data sets. The assimilation experiments performed here demonstrate for the first time the benefit of using satellite data to improve estimates of tropospheric ozone. / Ph. D.