Since the 1950s, a series of dams and levees have been constructed on the Missouri River to control seasonal flooding which had contributed to the fluctuation of the water level of Carter Lake.  The lake, no longer subject to an almost annual exchange of water to and from the Missouri River, has advanced into a hyper-eutrophic state, reducing its utility as a recreational lake and acting as the terminal end for contaminants received in an industrial, urban, suburban, and agricultural stormwater runoff.  Water quality has degraded and fluctuations in water quantity exacerbate the problem.

Carter Lake is on Nebraska’s Section 303(d) List of Impaired Waters for phosphorus, nitrogen, algae, chloryphyll, PCBs, and pH.  Additionally, the State of Iowa has determined that Carter Lake is impaired for ammonia, low dissolved oxygen, PCBs, algae toxins, phosphorus, nitrogen, and pH.  The primary water quality issues with the lake stem from high nutrient concentrations.  Elevated concentrations of phosphorus and nitrogen have contributed to blooms of blue green algae.  Toxins produced by blue-green algae resulted in lake postings that recommended against full body contact for 18 weeks during the 2004 through 2006 recreation seasons.  Carter Lake has also experienced occasional problems with bacteria.  High bacteria densities resulted in a Section 303(d) listing in 2004 but the listing was removed in 2005.