Hydrilla, although known for creating great fish cover, is a big problem for fishermen, boaters and other aquatic activity enthusiasts. Hydrilla can grow up to eight inches a day in clear water and can spread via tubers, turions and fragmentation. Since hydrilla can grow to lengths of 25 ft. (7.6 m) it can easily become tangled in boat motors. If boats are not cleaned properly, fragments of hydrilla can be introduced into new bodies of water. Dense populations of hydrilla can shade out native vegetation and raise pH and temperature of the water. Dense populations can also decrease oxygen levels beneath the mats and provide poor habitat for fish. Large populations of hydrilla may contain large numbers of fish; however, at high densities of fish the environment can only support a few harvestable-sized sport fish. Hydrilla also provides good breeding sites for mosquitoes, and interferes with swimming, water skiing and boating.

Zebra mussels were introduced, accidently, into the Great Lakes in 1988. They have now spread into several river systems in the South. Zebra mussels can reproduce very quickly, since females can lay more than 100,000 eggs per year! Individuals attach themselves to any hard, underwater surface, including boats and docks. Mussels pile on top of one another, creating thick "mats" of invaders. Zebra mussels can attach to hulls, increasing drag, and therefore increasing fuel costs. Small populations can clog boat cooling systems, causing boats to overheat. Populations can also disrupt boat motors that are not frequently used. The heat from frequently used motors keeps mussels from surviving. Large populations of zebra mussels can eat large amounts of plankton, thereby decreasing food availability for other aquatic inhabitants.

Grass carp (white amur) escaped from a fish farming experiment station in Stuttgart, Arkansas in 1966. This species, in sterile triploid form, is still introduced to control submersed aquatic weeds. Many problems with the sterilization process have been recognized and not all populations that have been released are sterile. Populations of grass carp are known in 45 states, with known reproductive populations in the Mississippi, Illinois, Missouri and Ohio rivers. Reproductive ability is very high, with an average female producing 500,000-700,000 eggs over her lifetime. Grass carp can live up to 10 years and can reach 80 pounds. Adults have an insatiable appetite and can consume 40-300% of their body weight of plant material every day. Large populations can clear all plant material from a body of water.

Aquatic vegetation provides habitat for juvenile fishes and invertebrates as well as acts as a stabilizer for bottom sediments. Loss of habitat for juvenile fishes and invertebrates causes many problems for fishermen. Eradication of aquatic vegetation causes murky water from the stirring of the sediment. Lack of vegetation also provides an opportunity for algal levels to increase, causing turbid water. The murky water is not aesthetically pleasing or beneficial to landowners or aquatic activity enthusiasts.

West Nile virus was first detected in the United States in 1999 and is spread by infected mosquitoes. People that spend time around standing bodies of water could be at risk of contracting this virus. Those who contract West Nile virus usually have mild flu-like symptoms or no symptoms at all. However, if the virus enters the brain it can cause the brain and spinal cord to swell and can lead to death. There are no specific vaccines or treatments available for the virus. So far in 2008 there have been 236 reported cases and 2 deaths caused by West Nile virus in the United States.