Manufactured nanomaterial production is outpacing the ability to investigate environmental hazard using current regulatory paradigms, causing a backlog of materials requiring testing. To ameliorate this issue, regulatory bodies have proposed integrating safety into the production of novel nanomaterials, allowing for hazards to be identified early in development rather than aftermarket release. In addition, there is a growing interest in short‐term ecotoxicity testing to rapidly identify environmental hazards. In this sense, the present study investigated 3 carbon nanofibers (CNFs), created with different production methods, using short‐term in vitro and in vivo exposures on fish cell lines, mussel hemocytes, crustacea, and algae. The present study investigated if differences in ecotoxicity hazard between the CNFs could be identified and, if so, which product could be considered less hazardous. A major challenge in assessing the potential hazards posed by manufactured nanomaterials is standardizing the preparation for testing. Standardized operating protocols have been proposed using protein to facilitate the preparation of stable stock suspension, which is not environmentally representative. As such, the study also assessed the potential impacts these standardized protocols (with or without the use of protein) could have on the interpretation of environmental hazard. The results demonstrated that there were clear differences between the 3 CNFs and that the dispersion protocol influenced the interpretation of hazard, demonstrating a need for caution when interpreting ecotoxicity in a regulatory context. Environ Toxicol Chem 2019;38:2314–2325. © 2019 SETAC.