Corporate Accountability International (CAI) revealed that the beverage giant will re-label the brand, which is sourced from a tap, as coming from a "Public Water Source" to address customer concerns over just what exactly they were drinking.
The move could lead to similar moves by other bottled water manufacturers, who face both the cost of re-labeling their products as well as a potential fall in sales.
Consumption of the product has benefited in recent years from increased consumer demand for more natural products non-carbonated beverage products.
PepsiCo explained that the decision would help ensure there was no confusion over where their bottled water was originating.
"If this helps clarify the fact that the water originates from public sources, then it's a reasonable thing to do," explained Michelle Naughton, a Pepsi-Cola North America spokeswoman speaking to the CNN news agency on Friday.
The move was welcomed by (CAI), which claimed that consumers might be misled by Aquafina's current labelling.
CAI said that the label, which depicts a snow-capped mountain along with the phrase "pure water, perfect taste" , was implying that the water came from a natural source before treatment.
The group added that Pepsi's example on revealing its source would be important in maintaining confidence amongst consumers over bottled water.
"Concerns about the bottled water industry, and increasing corporate control of water, are growing across the country," stated the CAI.
"It is significant that Pepsi is taking some action, especially since Aquafina is the leading bottled water brand in the US."
However, CAI added that PepsiCo was not alone in the practice of using the tap as a source for its goods, claiming that that about 40 per cent of all bottled water brands are sourced in this way.
Not everyone in the industry believes that PepsiCo's actions over labelling are necessary though.
The International Bottled Water Association (IBWA) claims that that under the regulations of the US Food and Drug Administration (FDA), public water systems like taps, have long been approved as a source for the product.
As such, it continued to support the FDA's view that water sourcing should not be an issue as long as products comply with its regulations on quality and safety.
The news regarding sourcing could come as a blow for the bottled water industry, which has undergone significant growth in sales over recent years.
Environmental researchers, Worldwatch, said the growing trend towards non-carbonated healthier drinks has led to an increase in the demand for bottled water.
As such global consumption has doubled between 1997 and 2005, reaching $10bn (€7.4bn) in the US alone, according to its estimates.
The industry is already experiencing some backlash in US restaurants over concerns that bottled water packaging may be contributing significantly to climate change.
Some establishments are encouraging consumption of tap water instead.