Mr Bolton was speaking at a news conference in Jerusalem when he sent the stark message to Syria ahead of its imminent offensive.
The National Security Adviser revealed US officials were aware of plans in which the Syrian government was considering to “resume offensive military activities”.
He said: “We are obviously concerned about the possibility that Assad may use chemical weapons again.
“Just so there’s no confusion here: if the Syrian regime uses chemical weapons, we will respond very strongly, and they really ought to think about this a long time.”
Mr Bolton argued the US ought to use “leverage” over Russia, one of President Assad’s two key backers, to force it to oust Iranian troops.
But Rick Sterling, an investigative journalist and member of the Syria Solidarity Movement, told Radio Sputnik’s Loud & Clear on Wednesday that the 69-year-old Baltimore native’s statement was “just another violation of international law”.
Sterling said: “It’s a threat that the US will use force.
“It’s another unauthorised assertion that the US is the judge, jury and executioner of the violations of the chemical weapons treaty.”
Sterling claimed the US had no authority to assert its dominance in this way.
The journalist insinuated that former US President Barack Obama was partly culpable for Syria’s current situation after he made his “red line” remark in 2012.
He said: “When President Obama made his statement, saying that chemical weapons moving around or being utilised was the red line, that was seen as the opportunity for the opposition groups to create some kind of incident.”
A year after in August, a sarin attack in the eastern Ghouta suburb of Damascus killed more than 1,500 people, including hundreds of infants.
In the aftermath of the incident, hundreds of images surfaced online showing the devastation and chaos in the region.
Following the backlash, Mr Obama gave another speech in which he suggested the US should intervene.
However, he argued Congress should give the go-ahead to proceed with any military intervention.
But when the Trump administration came into power, the mood changed.
Mr Trump responded with the full force of the US military after chemical attacks were reported in Syria.
In April 2017, Mr Trump, along with France and the UK, launched combined missile strikes on Syrian targets.
A total of 59 Tomahawk cruise missiles were deployed from the Mediterranean Sea into Syria.