Herein we describe the binding abilities of Zn(II) complexes of [12]aneN4- (L1) and [9]aneN3-based receptors (L2, L3) towards the herbicides N-(phosphonomethyl)glycine (glyphosate, H3PMG) and 2-amino-4-[hydroxy(methyl)phosphoryl]butanoic acid (glufosinate, H2GLU), and also aminomethylphosphonic acid (H2AMPA), the main metabolite of H3PMG, and phosphate. All ligands form stable Zn(II) complexes, whose coordination geometries allow a possible interaction of the metal center with exogenous anionic substrates. Potentiometric studies evidenced the marked coordination ability of the L2/Zn(II) system for the analytes considered, with a preferential binding affinity for H3PMG over the other substrates, in a wide range of pH values. 1H and 31P NMR experiments supported the effective coordination of such substrates by the Zn(II) complex of L2, while fluorescence titrations and a test strip experiment were performed to evaluate whether the H3PMG recognition processes could be detected by fluorescence signaling.