Disadvantages on the environment

The two traits being introduced to crops; herbicide tolerant (HT) and insects tolerant (Bt).
Herbicide tolerant (HT) involves altering the genes of the plant so that they are resistant to a very strong herbicide.
Insects tolerance (Bt), involves having the plant to produce the insecticide themselves so as to reduce the need of spraying pesticides. This is done by introducing a Bt gene into the plant. Bt gene is a gene from a bacterium that can produce natural insecticides.

Harming other insects

GM crops such as Bt corn helps to eliminate the problem of crop harming pests. Since there is no way to make Bt crop kill only the crop harming pest whenever a pollen of the Bt crop landed on a natural habitat it may wipe out a number of species of insects that were not targeted.

Stronger Pests and weeds

GM crops mostly have a short lifespan because the Bt crops are always overused. When the Bt crops are overused it will lose it effectiveness against the pests and virus. Insects and viruses will evolve into stronger species that are resistant to the pesticides.
Weeds have also evolved to become herbicide resistant; an example would be mare’s tail (resistant horseweed), the weed was known to resistant to glyphosate. The Glyphosate resistant horseweed showed up in soybeans and cotton and was spreading quickly through the United States.

Soil Toxicity

Since the GM crops are resistant to toxic herbicides and pesticides it means that stronger herbicides and pesticides and be introduced to the crops and they could be sprayed onto the entire crops rather than just on the weeds. The large amounts of herbicides and pesticides sprayed will result in soil toxicity. These herbicides leaches out into rivers and ponds causing excessive growth of weeds until the surface of the ponds are completely covered; plants in the ponds will not get enough sunlight for photosynthesis to produce oxygen for the organisms living in the pond.

Pesticides stay in the soil for many years, degrading the quality of the soil. It will also affect the animals like birds, chicken that feed on insects that live in/ on the insecticides and eventually affecting us, after consuming the affected animals.