The difficulty of assessing risk of sediment-associated contaminant mixtures to benthic ecosystems is often attributed to understanding the bioavailable fraction of each contaminant. These issues have led to the development of the toxicity identification evaluation (TIE). Past pore water TIE testing on Illinois River sediments has indicated that ammonia was the primary contaminant. The current study, however, suggests that ammonia is no longer the primary contaminant of concern, but rather non-polar organics, including polycyclic aromatic hydrocarbons, are the primary cause for toxicity in the Illinois River Complex (IRC). Summer of 2007 testing showed that six out of the seven sites that proceeded to Phase I testing exhibited a significant increase in survival with the addition of the non-polar organic amendment powdered coconut charcoal (PCC), while zeolite (ammonia amendment) and Resin Tech SIR 300 (cationic metals amendment) did not significantly increase survival suggesting that non-polar organics are the source of toxicity. In addition, Phase II testing suggested that concentrations of PAHs were high enough to cause the observed toxicity, which confirmed the results of Phase I testing. Additional seasonal-based sampling (i.e., fall, winter, spring, and summer 2008) supported the summer findings, with little variation between toxicity and concentrations, with 46% of the sites being improved with the addition of PCC in Phase I testing. The results of Phase I and Phase II contradicted past pore water TIE studies as non-polar organics were suggested as the source of toxicity rather than ammonia. Thus, both pore water and whole sediment TIE methodologies were used on two selected sites. The results of this study suggested that discordance between the past pore water TIEs and the current whole sediment TIE were attributed to the methodologies and on a lesser note the test organisms used. The present study provides data that could be used in combination with previous work to more accurately characterize the sources and spatial trends of toxicity in Illinois River sediments for future risk assessment and mitigation. Furthermore, the present study showed that while TIE methodologies are a valuable tool in assessing risk associated with contaminants in aquatic system, further research in understanding the role that each TIE method may serve in risk assessment is also important.