Abstract In this paper, we use Atangana–Baleanu derivative which is defined with the Mittag–Leffler function and has all the properties of a classical fractional derivative for solving the system of fractional differential equations. The classical model of polluted lakes system is modified by using the concept of fractional differentiation with nonsingular and nonlocal fading memory. The new numerical scheme recommended by Toufik and Atangana is used to analyze the modified model of polluted lakes system. Some numerical illustrations are presented to show the effect of the new fractional differentiation.