We prove that any Fourier--Mukai partner of an abelian surface over an algebraically closed field of positive characteristic is isomorphic to a moduli space of Gieseker-stable sheaves. We apply this fact to show that the Fourier--Mukai set of canonical covers of hyperelliptic and Enriques surfaces over an algebraically closed field of characteristic greater than three is trivial. These results extend to positive characteristic earlier results of Bridgeland--Maciocia and Sosna.