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ABSTRACT Ditches are essential elements of the agricultural landscape because of their role as habitat or refuge for aquatic species, especially in homogenized and intensively cultivated areas. However, data on the biodiversity associated with agricultural ditches, and its variation over time, are underrepresented in ecological research. This study aimed at quantifying the inter‐annual changes in the alpha and beta diversity of benthic macroinvertebrate communities across five agricultural ditches in the lowland, agricultural area of the Novara Province (northwestern Italy). Benthic macroinvertebrates were always sampled in October but in two different years: 2022 and 2023, respectively. These two years differed in the climate and hydrological conditions with lower precipitations and discharge in 2022 than 2023. The alpha diversity metrics, such as taxon richness, total abundance, Ephemeroptera, Plecoptera and Trichoptera richness and abundance, and Shannon index, were significantly higher in 2023 than in 2022. Moreover, these metrics were positively correlated with the water velocity, and negatively correlated with the concentration of phosphates. Benthic macroinvertebrate communities in 2022 showed higher beta diversity compared to 2023, with significant differences in the taxonomic composition. By controlling for the season, the results here obtained demonstrate that ditch macroinvertebrate communities are responsive to temporal variability in hydrological, climate, and environmental conditions with changes in the taxonomic diversity and composition driven by water velocity and nutrient enrichment. As agricultural ditches are still poorly monitored, this study provides science‐based information and potential insights for their sustainable management.