The City of Chicago does not yet have an isolated wetland regulations, although there is one being worked on, so I am only looking at this from a 404 perspective:
Is an industrial wastewater treatment pond that has been inactive for several years, but has a pipe outlet to a Water of the US considered a Water of the US itself (is it regulated)? It has wetland vegetation growing in/among it now.

From the Waters of the US definition:
7. Wetlands adjacent to waters (other than waters that are themselves wetlands) identified in paragraphs (a)(1)-(6) of this section.
Waste treatment systems, including treatment ponds or lagoons designed to meet the requirements of CWA (other than cooling ponds as defined in 40 CFR 123.11(m) which also meet the criteria of this definition) are not waters of the United States.

If the pond is still legally useable, one usage would make it not subject to corps jurisdiction.
If it was abandoned, perhapse the corps will use gravel pit abandonment as a guide. I think it is 5 years abandonment before a created wetland becomes subject to jurisdiction. If this sewage pond was a wetland before it treated sewage, I think it is jurisdictional as soon as the sewage stopped.