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Preserved biological communities can provide baseline data about the historical ecosystems and environmental conditions that preceded recent anthropogenic alteration. Freshwater mussel shells show particularly good preservation, and the shell assemblages commonly found during archaeological excavations can offer insights into past ecosystems. We studied assemblages of Unio pictorum mussel shells from palaeochannel silts associated with the Late Bronze Age site of Must Farm in eastern England (c. 850 BC), on an ancient tributary of the modern-day River Nene. We compared archaeological shells from two sediment horizons (broadly 1300-700 BC) to live individuals collected from two analogous sites on the present-day Nene. Size and growth rate, interannual growth variability and stable isotope (δ 18 O and δ 13 C) composition were compared between the populations. Size and the von Bertalanffy growth parameter L ∞ differed among all four populations. Mean lengths and L ∞ were higher in the two modern populations (mean lengths 77.3 ± SE 0.8 and 73.8 ± SE 1.1 mm, L ∞ 91.8 ± 5.4 and 79.0 ± 8.1 mm) than the ancient populations (mean lengths 58.1 ± SE 1.6 mm and 68.4 ± SE 0.9 mm; L ∞ 71.5 ± 16.9 and 76.8 ± 6.2 mm). Modern individuals also showed greater variation in age-corrected year-to-year growth. δ 13 C was lower in modern shells (-11.8‰ for modern shells, -9.03‰ and -9.02‰ for ancient shell populations), potentially reflecting altered hydrological and nutrient regimes. δ 18 O and δ 13 C were positively correlated for all but one sampled ancient shell, but not modern shells. These results reflect changes in local environmental conditions, particularly the transition from a shallow, slow-flowing tributary to a deeper, canalised river with faster flow, as well as effects of anthropogenic nutrient enrichment. The findings demonstrate the importance of long-term data in studying anthropogenic ecosystem alteration and avoiding shifting baseline syndrome in conservation planning., (Global Change Biology© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)