Many topological semimetals are known to exhibit exceptional electronic properties, which are the fundamental basis for design of novel devices and further applications. Materials containing the structural motif of a square net are known to frequently be topological semimetals. In this work, the synthesis and structural characterization of the square‐net‐based magnetic topological semimetal candidates GdSbxTe2−x−δ (0≤x≤1, δ indicating the vacancy level) are reported. The structural evolution of the series with Sb substitution is studied, finding a transition between a simple tetragonal square‐net structure to complex superstructure formations due to the presence of charge density waves. The structural modulations coincide with a significant modification of the magnetic order. This work thus establishes GdSbxTe2−x−δ as a platform to study the interplay between crystal symmetry, band filling, charge density wave, and magnetism in a topological semimetal candidate.