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Eutrophication erodes inter-basin variation in macrophytes and co-occurring invertebrates in a shallow lake: combining ecology and palaeoecologyAquatic biodiversity is commonly linked with environmental variation in lake networks, but less is known about how local factors may influence within-lake biological heterogeneity. Using a combined ecological and multi-proxy palaeoecological approach we investigated long-term changes in the pathways and processes that underlie eutrophication and water depth effects on lake macrophyte and invertebrate communities across three basins in a shallow lake—Castle Lough, Northern Ireland, UK. Contemporary data allow us to assess how macrophyte assemblages vary in composition and heterogeneity according to basin-specific factors (e.g. variation in water depth), while palaeoecological data (macrophytes and co-occurring invertebrates) enable us to infer basin-specific impacts and susceptibilities to nutrient-enrichment. Results indicate that variability in water depth promotes assemblage variation amongst the lake basins, stimulating within-lake macrophyte assemblage heterogeneity and hence higher lake biodiversity. The palaeo-data indicate that eutrophication has acted as a strong homogenising agent of macrophyte and invertebrate diversities and abundances over time at the whole-lake scale. This novel finding strongly suggests that, as eutrophication advances, the influence of water depth on community heterogeneity is gradually eroded and that ultimately a limited set of eutrophication-tolerant species will become homogeneously distributed across the entire lake.