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Still, despite the challenges, the ACA and its associated regulations will make a tremendous difference, particularly among those populations disproportionately affected by substance abuse.

"I think that the ACA is an absolute game changer," Donner said. "And I'm extremely excited about the potential of it."

One of the most important changes in the ACA may come from its larger philosophical implications, Heller said. Essentially, President Obama's health care act enshrines in federal law that substance abuse is a medical issue--not the result of poor morals, and not a criminal justice problem, Heller said.

That reflects a greater societal change, as the country as a whole has gotten over some of the stigma it once held for substance abuse, Bianchi said. "This is a shift that has taken place over generations," he said. "It's not just a matter of a couple of years and a couple of laws."

The ACA's federal definition of addiction as a healthcare issue may even pave the way to greater changes, potentially including decriminalization, Heller said.

"If we view ACA as this document that is now federal's sort of de facto recognition that it's not a criminal justice issue. It needs to be addressed as a health issue."