An ecological risk assessment framework for aircraft overflights has been developed, with special emphasis on military applications. This article presents the analysis of effects and risk characterization phases; the problem formulation and exposure analysis phases are presented in a companion article. The framework addresses the effects of sound, visual stressors, and collision on the abundance and production of wildlife populations. Profiles of effects, including thresholds, are highlighted for two groups of endpoint species: ungulates (hoofed mammals) and pinnipeds (seals, sea lions, walruses). Several factors complicate the analysis of effects for aircraft overflights. Studies of the effects of aircraft overflights previously have not been associated with a quantitative assessment framework; therefore no consistent relations between exposure and population-level response have been developed. Information on behavioral effects of overflights by military aircraft (or component stressors) on most wildlife species is sparse. Moreover, models that relate behavioral changes to abundance or reproduction, and those that relate behavioral or hearing effects thresholds from one population to another are generally not available. The aggregation of sound frequencies, durations, and the view of the aircraft into the single exposure metric of slant distance is not always the best predictor of effects, but effects associated with more specific exposure metrics (e.g., narrow sound spectra) may not be easily determined or added. The weight of evidence and uncertainty analyses of the risk characterization for overflights are also discussed in this article.