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The current existence of that domain name should have been enough warning. But in case it wasn't, here is a list of just the aquatic imported species that the US government says have already had a significant negative impact on our environment: http://www.invasivespeciesinfo.gov/aquatics/main.shtml#aqan

Side note: There is an entire domain directed at the difference between affect and effect; please educate yourself.

To respond to your comment: biological agents are extremely problematic. Aside from the obvious issues involved with targeting an herbicide (biological or other) at a specific plant, there are numerous environmental disasters that were caused explicitly by introducing a new species into an area as a biological control method. The National Invasive Species Information Center has information on a large number of critters imported to areas as a control for other pests which then took over and dramatically altered the biodiversity of the area. For a specific example, try a Google search for the Cane Toad, or look to the Wikipedia article for an idea of how quickly and badly things can go wrong. For example, the following excerpt from that article:

Around 150 cane toads were introduced to Oahu in Hawaii in 1932, and the population swelled to 105,517 after 17 months.

You see, the cane toad had plenty of food and no natural predators in its new environment, so in less than a year and a half it rapidly took over the entire region, expanding its population literally a thousandfold. This was an unexpected "side effect" of attempting to control a beetle infestation in the crops by importing the toads. Another unanticipated issue was the toads' defense mechanism:

The adult cane toad has enlarged parotoid glands behind the eyes, and other glands across their back. When the toads are threatened, their glands secrete a milky-white fluid known as bufotoxin. Components of bufotoxin are toxic to many animals; there have even been human deaths due to the consumption of cane toads.
Bufotenin, one of the chemicals excreted by the cane toad, is classified as a Class 1 drug under Australian law, alongside heroin and cannabis. It is thought that the effects of bufotenin are similar to that of mild poisoning; the stimulation, which includes mild hallucinations, lasts for less than an hour. As the cane toad excretes bufotenin in small amounts, and other toxins in relatively large quantities, toad licking could result in serious illness or death.

In other words, the damn things are extremely poisonous. The fact that one of the toxins they excrete induces hallucinations actually made the problem worse, as people would seek them out for a cheap thrill, and then end up in the hospital (or even the morgue) because they licked a toad to get high. Making the toxin a controlled substance didn't really help, and may have actually made the issue worse due to the Streisand Effect ("That's weird... why would they make it illegal to lick a toad? Oh, hey...")

In short, "biological agents" are generally considered to be a Bad Thing (tm).

Under similar circumstances in Australia the CSIRO http://www.csiro.au/science/PestManagement.html , would investigate the weed species, find it's country of origin, find insects, bacteria or fungi that feed on it and then bring back samples under controlled conditions. These species would then be tested against Australian native plants and commercial species and those imported species that do not predate upon those would then be tested for survivability in the regions most affected by the weed species. Once the optimum control species are found they are released into the environment to control the weed species.

Although this is by far the most cost effective method of control it often not very popular in capitalism first, last and everything in between countries as there is no opportunity for profit in the solution as it must be given away free, to spread on it's own. In the case of the US the USDA http://www.invasivespeciesinfo.gov/ is the likely agency that should be working on those problems on a federal basis. So rather than throwing away money on spraying and, spraying and, spraying, better to pursue the USDA and get them working on long term biological solutions, where it is all about saving money while saving the environment.

That and for the few species that have benefited, there's plenty that have not and a result of the cleaner water means the growth of weeds has exploded.

Ah, one of those invasive species, "weeds", is Kudzu, another invasive species from Asia. The problem with invasive species is that they over compeat with native species.

However, I think it's fair to argue that ideas such as "economy," "jobs," and "government" , and the industrialization that comes with them, are far from natural. So if we as a race are going to disrupt things that are clearly natural (i.e., species survival), we can't justify those actions through natural selection.

Actually, people are concerned anytime a new strain or species (whether natural or GM) is introduced to the local ecosystem. Sometimes there's no major effects. Sometimes, it turns into an invasive species.

http://www.invasivespeciesinfo.gov/unitedstates/ma in.shtml