Elimination of nitrogenous byproducts of metabolism from the body is called excretion. Amoeba lacks special organelles and arrangement for it. Principal excretory by product is ammonia (ammonotelic). Like CO2 , ammonia also continuously diffuses out in solution, through plasmalemma, because its concentration is always higher in the body than in surrounding water. Further, the crystals, called biurets (bipyramidal) and triurets (tripyramidal), found regularly in the endoplasm, are formed of an excretory substance, carbonyldiurea. Possibly, Amoeba stores most of its nitrogenous byproducts in the form of these crystals. When and how Amoeba gets rid of these in not known.
Since, freshwater is hypotonic to the cytoplasm of Amoeba, there is a continuous endosmosis or in flow of water into the body. Also, some water is added to the cytoplasm from food vacuoles and from catabolic reaction. At all this water is allowed to accumulate, the body will soon swell and burst. Hence, all freshwater protozoans, including Amoeba, possess one or two contractile vacuoles for elimination of excess water from the body, ie, osmoregulation. Amoeba has only one contractile vacuole. The vacuole regularly pumps out excess water.