It's easy to assume that just because hamsters do well in aquariums that guinea pigs would too. That isn't the case. Because of the guinea pig's larger size, there are a number of issues that can arise. Not only is air circulation poor in aquariums, but the size needed for a guinea pig can make aquariums difficult to clean.
Air Circulation
Air circulation is important for rodents, and rodents as large as guinea pigs cannot get enough ventilation in an aquarium. When there isn't enough ventilation, upper respiratory infections can occur, the temperature is harder to regulate, and the odor of the habitat will be much worse than if you kept the pet in a cage.
Size
A fully grown guinea pig measures 8 to 12 inches in length. Because of this large size, you would need a habitat that is at least 30 by 36 inches. If you choose to house two guinea pigs, the size would need to be 30 by 50 inches. In terms of aquariums, that's roughly a 50 to 75 gallon tank. This large size makes it nearly impossible to thoroughly clean the habitat.
Proper Housing
A proper guinea pig habitat is either a cage or hutch. Cages and hutches let in enough ventilation, but must be properly closed to keep your pet from escaping. Note that most cages that are labeled as guinea pig habitats are not large enough to give your pet enough room. Always purchase a case based on the size, not the labels. When shopping for a cage, make sure it has a well-fitting bottom and is hard to open. If you're buying a hutch, remember that guinea pigs cannot be kept outside or in the garage.
(Source: http://animals.mom.me/can-guinea-pig-stay-aquarium-1377.html)
I purchased a guinea pig in Sept 2014 who came home with severe skin issues and an upper respiratory infection from the aquarium that she was living in. Just last week, I adopted a guinea pig from a local Petco who had part of her ear chewed off, and was missing a toe. We took her home, and put her in quarantine (we have 7 other guinea pigs) and it turns out that she has an upper respiratory infection! Petco has a '30 day' policy to return. I called the store who said I'd have to return her, then they keep her in possession until the vet sees her and treats (up to a month!) I didn't care for this as she is a baby, and I didn't want to put her through the thought of feeling abandoned. We decided to take her back to our vet, and provide treatment. If she was in proper caging during her time at the pet store, this wouldn't have been an issue. Please research and provide the proper care for these pets so potential owners won't turn away when they see a sick guinea pig, or get the idea that an aquarium is proper housing for them.