Increasing use of carbon nanotubes (CNTs) in consumer and industrials goods increases their potential release, and subsequent risks to environmental and human health. Therefore, it is becoming ever more important that CNTs are designed to reduce or eliminate hazards and that hazard assessment methodologies are robust. Here, oxygen-functionalized multi-walled CNTs (O-MWCNTs), modified under varying redox conditions, were assessed for toxic potential using the zebrafish (Danio rerio) embryo model. Multiple physicochemical properties (e.g., MWCNT aggregate size, morphology, and rate; surface charge and oxygen concentration; and reactive oxygen species (ROS) generation) were characterized and related to zebrafish embryo mortality through the use of multivariate statistical methods. Of these properties, surface charge and aggregate morphology emerged as the greatest predictors of embryo mortality. Interestingly, ROS generation was not significantly correlated to observed mortality, contrary to prior predictions by nanotoxicology researchers. This suggests that the mechanism of MWCNT-induced mortality of embryonic zebrafish is physical, driven by electrostatic and shape effects, both of which are related to nanomaterial aggregation. This raises the importance of rigorously considering aggregation during aqueous-based nanotoxicology assays as nanomaterial aggregation can affect perceived nanomaterial toxicity. As such, future nanotoxicity studies relying on aqueous media must sufficiently consider nanomaterial aggregation.