The EPA Office of Water’s National Coastal Condition Assessment (NCCA) helps satisfy the assessment and antidegradation provisions of the Clean Water Act by estimating water, sediment, and benthic quality conditions in the Great Lakes nearshore on a five-year cycle starting in 2010. Beginning in the 2015 NCCA cycle, the connecting channels of the Huron-Erie corridor (HEC; 2014, 2015) and St. Marys River (SMR; 2015, 2016) were assessed through a partnership with Great Lakes National Program Office and Office of Research and Development. Great Lakes connecting channels include Areas of Concern (AOCs) designated under the Great Lakes Water Quality Agreement due to legacy contamination and are the focus of ongoing remediation and restoration efforts. The NCCA probabilistic survey design allows estimates of current conditions for water, benthic, and sediment quality. While preliminary results from water and sediment indices demonstrate the challenges associated with applying the NCCA indices in the connecting channels, we use comparisons of sediment chemistry results from the probability-based sampling to results from targeted sediment chemistry studies to highlight the value of system-wide assessment. Probability-based sampling is a tool with potential to aid in the design of restoration efforts related to AOCs and for assessment of restoration success in the connecting channels.