New aspects and advancements in classical uncertainty propagation methods were used to develop a nutrient budget with associated uncertainty for a northern Gulf of Mexico coastal embayment. Uncertainty was calculated for budget terms by propagating the standard error and degrees of freedom. New aspects include the combined use of Monte Carlo simulations with classical error propagation methods, uncertainty analyses for GIS computations, and uncertainty propagation involving literature and subjective estimates of terms used in the budget calculations. The methods employed are broadly applicable to the mathematical operations employed in ecological studies involving step-by-step calculations, scaling procedures, and calculations of variables from direct measurements and/or literature estimates. Propagation of the standard error and the degrees of freedom allowed for calculation of the uncertainty intervals around every term in the budget. For scientists and environmental managers, the methods developed herein provide a relatively simple framework to propagate and assess the contributions of uncertainty in directly measured and literature estimated variables to calculated variables. Application of these methods to environmental data used in scientific reporting and environmental management will improve the interpretation of data and simplify the estimation of risk associated with decisions based on ecological studies.