The recruitment of American eel (Anguilla rostrata) juveniles to Lake Ontario (LO), Canada has declined significantly since the 1980s. To investigate the possible contribution of maternally-transferred persistent organic pollutants (POPs) to this decline, this study measured temporal variations in the toxicity of complex organic mixtures extracted from LO American eels captured in 1988, 1998 and 2008 to developing Fundulus heteroclitus exposed by intravitelline (IVi) injection. The 1988 and 1998 eel extracts were most toxic, causing a pattern of sublethal embryotoxic responses similar to those previously reported in F. heteroclitus embryos exposed to single dioxin-like compounds (DLCs): stunted growth, craniofacial deformities, EROD activity induction, and reduced predatory capacities. The potency of extracts declined over time; the only significant effect of the 2008 eel extracts was EROD induction. The chemically-derived TCDD-TEQs of eel extracts, calculated using measured concentrations of some DLCs and their relative potencies for F. heteroclitus, overestimated their potency to induce EROD activity possibly due to interactions among POPs. Other POPs measured in eel extracts (non-dioxin-like PCBs, PBDEs and organochlorinated pesticides) did not appear to be important agonistic contributors to the observed toxicity. The toxicity of the complex mixtures of POPs measured in LO eels may have been underestimated as a result of several factors, including the loss of POPs during extracts preparation and a focus only on short-term effects. Based on the model species examined, our results support the hypothesis that contamination of LO with DLCs may have represented a threat to the American eel population through ecologically-relevant effects such as altered larval prey capture ability. These results prioritize the need to assess early life stage (ELS) toxicity of DLCs in Anguilla species, to investigate long-term effects of complex eel extracts to ELS of fish, and to develop biomarkers for potential effects in eel ELS sampled in the field.