Toxicity reference values (TRVs) are essential in models used in the prediction of the potential for adverse impacts of environmental contaminants to avian and mammalian wildlife; however, issues in their derivation and application continue to result in inconsistent hazard and risk assessments that present a challenge to site managers and regulatory agencies. Currently, the available science does not support several common practices in TRV derivation and application. Key issues include inappropriate use of hazard quotients and the inability to define the probability of adverse outcomes. Other common problems include the continued use of no-observed-and lowest-observed-adverse-effect levels (NOAELs and LOAELs), the use of allometric scaling for interspecific extrapolation of chronic TRVs, inappropriate extrapolation across classes when data are limited, and extrapolation of chronic TRVs from acute data without scientific basis. Recommendations for future TRV derivation focus on using all available qualified toxicity data to include measures of variation associated with those data. This can be achieved by deriving effective dose (EDx)-based TRVs where x refers to an acceptable (as defined in a problem formulation) reduction in endpoint performance relative to the negative control instead of relying on NOAELs and LOAELs. Recommendations for moving past the use of hazard quotients and dealing with the uncertainty in the TRVs are also provided.