Phosphonates contain one or more C–PO(OH)2 groups and function as human complexing agents. Chelating agents and scale inhibitors are two of their many industrial and technical uses. Phosphonates are distinguished from other chelating agents by characteristics that have a significant impact on their behavior in the environment. Phosphonates have a significant removal in both natural and technological systems due to their strong interaction with surfaces. Because of this solid adsorption, practically zero remobilization of metals is normal. Phosphate is not broken down by biodegradation during water treatment, but the Fe(III)-complexes are broken down quickly by photo degradation. In the presence of Mn(II), aminopolyphosphonates also undergo rapid oxidation, resulting in the formation of oxygen and stable breakdown products that have been observed in wastewater. Analytical difficulties in determining phosphonates at trace concentrations in natural waters are to blame for the lack of environmental information. In this area, further method development, including speciation of these compounds, is urgently required. Based on the current understanding of speciation, we can conclude that phosphonates have no effect on metal speciation or transport because they are mostly Ca and Mg-complexes in natural waters.