Polycyclic aromatic hydrocarbons (PAHs) and metal(loid) mass flux estimates and forensic assessment using PAH diagnostic ratios were used to inform remediation decision making at the Sydney Tar Ponds (STPs) and Coke Ovens cleanup project in eastern Canada. Environmental effects monitoring of surface marine sediments in Sydney Harbor indicated significantly higher PAH concentrations during the first year of remediation monitoring compared to baseline. This was equivalent to PAH loadings of ∼2,000 kg over a 15‐month period. Increases in sediment PAH concentrations raised serious concerns for regulators, who requested cessation of remediation activities early in the $400 M (CAD) project. Historically, the STPs were reported as the primary source of PAH contamination in Sydney Harbor with estimated discharges of 300 to 800 kg/year between 1989 and 2001. Mass flux estimates of PAHs and metal(loid)s and PAH diagnostic ratios were used to evaluate if increases in PAH concentrations in marine sediments were the result of the STPs remediation activities. PAH mass flux estimates approximated that 17 to 97 kg/year were discharged from the STPs during three years of remediation and were corroborated by an independent PAH flux estimate of 119 kg in year 1. PAH fluxes to the Sydney Harbor were mostly surface water derived, with groundwater contributing negligible quantities (0.002–0.005 kg/year). Fluxes of metal(loid)s to harbor sediments were stable or declining across all years and were mirrored in sediment metal(loid) concentrations, which lacked temporal variation, unlike total PAH concentrations. Flux results were also corroborated using PAH diagnostic ratios, which found a common source of PAHs. Coal combustion was likely the principal source of PAHs and not migration from the STPs during remediation. Although short‐term residual sediment PAH increases during onset of remediation raised concerns for regulators, calls for premature cessation of remediation early in the project were unwarranted based on only one year of monitoring data. Mass flux estimates and forensic assessments using PAH diagnostic ratios proved useful tools to inform remediation decision making that helped environmental protection and reduced costs associated with lost cleanup time.