In vegetated filter strips (VFS) the presence of perennial vegetation, rhizodeposition of labile organic substrates and the accumulation of an organic residue thatch layer may enhance microbial numbers and activity, thereby increasing the potential for mineralisation of herbicides and herbicide metabolites retained during run-off events. The objective of this laboratory experiment was to compare the mineralisation of atrazine and metolachlor with that of their respective metabolites in VFS and cultivated soil. With the exception of total bacteria, propagule density of the microbial groups, endogenous soil enzymes and microbial diversity were higher in the VFS soil. This correlated with increased mineralisation of metolachlor and its metabolites in the VFS soil and indicates potential for VFS to curtail the subsequent transport of these compounds. In contrast, the mineralisation of atrazine and the majority of its metabolites was substantially reduced in VFS soil relative to cultivated soil. Consequently, the potential for subsequent transport of atrazine and many of its metabolites may be greater in VFS soil than in cultivated soil if reduced mineralisation is not offset by increased sorption in the VFS.