Factory legacy pollutants are an increasing concern for waterways as old infrastructure deteriorates and contaminates nearby environments. The Fisherville Mill in Grafton, Massachusetts, USA exemplifies this problem since it has now fallen into disrepair and is leaking Bunker C crude oil into the adjoining Blackstone River, a third order stream. Our research examines how effectively an ecologically engineered system (EES), consisting of anaerobic bacteria environments, fungal microcosms, and aquatic plant environments, can break down petroleum hydrocarbons, specifically aliphatic and polycyclic aromatic hydrocarbons (PAH), in this river environment. Our testing protocol involved taking water samples before and after each filtration stage monthly from June through October 2012. Water samples were analyzed at the Brown University Superfund Research Lab using mass spectrometry to determine aliphatic and PAH concentrations. Post-treatment aliphatic oil concentrations were significantly different from baseline concentrations (p=0.005), with an average reduction of 95.2%. Post-treatment PAH concentrations were also significantly different from baseline concentrations (p=0.001), with an average reduction of 91%. We conclude that this EES provided effective treatment for Bunker C crude oil, even though some filtration stages did not achieve their intended objectives. This type of filtration arrangement might be scaled up for use in larger remediation efforts regarding Bunker C crude oil.