Riparian vegetation is known to affect aquatic macroinvertebrate communities through contributions of organic matter and shading. Despite the widespread degradation of riparian vegetation in Australia, there are relatively few studies examining the effect of changes in riparian vegetation on in-stream macroinvertebrate assemblages on individual catchments. In particular, information is lacking on the responses of macroinvertebrate communities in catchments dominated by agriculture, where farms that are managed at the paddock scale result in riparian vegetation condition varying over relatively short distances. In this study, macroinvertebrate assemblages were assessed from 12 reaches along a 25-km section of a small agricultural stream in southeastern Australia. Riparian condition was assessed using in-stream coarse woody debris (CWD) levels and the rapid appraisal of riparian condition (RARC) index, a numerical system for categorising the health of riparian areas that incorporates sub-indices reflecting habitat continuity, vegetation cover, plant debris levels, native vegetation dominance, and other indicative features. There was a significant positive correlation between RARC scores and macroinvertebrate taxon richness (p < 0.01), and also between CWD scores and macroinvertebrate taxon richness (p < 0.05). In contrast, there was no significant correlation observed between riparian condition and the other macroinvertebrate indices (abundance, Shannon diversity, SIGNAL and SIGNAL2). Macroinvertebrate communities were significantly different in stream reaches from different riparian condition categories (ANOSIM; p < 0.05). Our results indicate that efforts to rehabilitate riparian vegetation may have a positive effect on in-stream biota even when implemented at a relatively small scale by individual landholders.