I don't know how much you know about tank cycling, but bacteria are the key to a healthy aquarium ecosystem. When you throw away established filter media, you throw away bacteria that actually do the filtering by breaking down harmful organic compounds into less harmful ones. Your cycle has been disrupted, and it takes time to allow the bacterial colonies to regenerate. In the meantime, you have to either remove the contaminants manually (water changes), or treat them to make them less harmful (Prime), preferably both. There are bacterial supplements available that supposedly jump-start the cycle in a new tank, but I don't use them myself and I've heard mixed reviews of them.