Computational fluid dynamics (CFD) simulations can provide tremendous insight into complex physical processes and are often faster and more cost-effective to execute than experiments. However, each CFD result inherently contains numerical errors that can significantly degrade the accuracy of a simulation. Discretization error is typically the largest contributor to the overall numerical error in a given simulation. Discretization error can be very difficult to estimate since the generation, transport, and diffusion of these errors is a highly nonlinear function of the computational grid and discretization scheme. As CFD is increasingly used in engineering design and analysis, it is imperative that CFD practitioners be able to accurately quantify discretization errors to minimize risk and improve the performance of engineering systems. In this work, improvements are made to the accuracy and efficiency of existing error estimation techniques. Discretization error is estimated by deriving and solving an error transport equation (ETE) for the local discretization error everywhere in the computational domain. Truncation error is shown to act as the local source for discretization error in numerical solutions. An equivalence between adjoint methods and ETE methods for functional error estimation is presented. This adjoint/ETE equivalence is exploited to efficiently obtain error estimates for multiple output functionals and to extend the higher-order properties of adjoint methods to ETE methods. Higher-order discretization error estimates are obtained when truncation error estimates are sufficiently accurate. Truncation error estimates are demonstrated to deteriorate on grids with a non-smooth variation in grid metrics (e.g., unstructured grids) regardless of how smooth the underlying exact solution may be. The loss of accuracy is shown to stem from noise in the discrete solution on the order of discretization error. When using conventional least-squares reconstruction techniques, this noise is exactly captured and introduces a lower-order error into the truncation error estimate. A novel reconstruction method based on polyharmonic smoothing splines is developed to smoothly reconstruct the discrete solution and improve the accuracy of error estimates. Furthermore, a method for iteratively improving discretization error estimates is devised. Efficiency and robustness considerations are discussed. Results are presented for several inviscid and viscous flow problems. To facilitate the study of discretization error estimation, a new, higher-order finite-volume solver is developed. A detailed description of the code base is provided along with a discussion of best practices for CFD code design. / Ph. D. / Computational fluid dynamics (CFD) is a branch of computational physics at the intersection of fluid mechanics and scientific computing in which the governing equations of fluid motion, such as the Euler and Navier-Stokes equations, are solved numerically on a computer. CFD is utilized in numerous fields including biomedical engineering, meteorology, oceanography, and aerospace engineering. CFD simulations can provide tremendous insight into physical processes and are often preferred over experiments because they can be performed more quickly, are typically more cost-effective, and can provide data in regions where it may be difficult to measure. While CFD can be an extremely powerful tool, CFD simulations are inherently subject to numerical errors. These errors, which are generated when the governing equations of fluid motion are solved on a computer, can have a significant impact on the accuracy of a CFD solution. If numerical errors are not accurately quantified, ill-informed decision-making can lead to poor system performance, increased risk of injury, or even system failure. In this work, research efforts are focused on numerical error estimation for the finite -volume method, arguably the most widely used numerical algorithm for solving CFD problems. The error estimation techniques provided herein target discretization error, the largest contributor to the overall numerical error in a given simulation. Discretization error can be very difficult to estimate since these errors are generated, convected, and diffused by the same physical processes embedded in the governing equations. In this work, improvements are made to the accuracy and efficiency of existing discretization error estimation techniques. Results are presented for several inviscid and viscous flow problems. To facilitate the study of these error estimators, a new, higher-order finite -volume solver is developed. A detailed description of the code base is provided along with a discussion of best practices for CFD code design.