Biogenic apatite preserved in 148 samples of conodonts and organophosphatic-shelled brachiopods from Cambrian through Ordovician successions of the Baltoscandian Basin (Baltica Plate) preserves a sensitive record of early Palaeozoic sea-water chemistry interpreted via neodymium isotope ratios. Consistent εNd(t) values of −9.6 to −8.3 for Lower to Middle Cambrian samples suggest no significant lateral or temporal variation across the region. Average Upper Cambrian values are −7.2 to −7.7. Sedimentary analysis suggests that the influence of continental weathering from Baltica as a major source of radiogenic Nd was negligible. Ordovician samples show a rise to −5 to −6 in the early Arenig, early–mid Llanvirn and late Caradoc. Sea-water mixing from the southeast Iapetus Ocean was a constant factor throughout Cambrian–Ordovician times. The rise reflects erosion of obducted volcanic arc complexes along the Caledonian margin, and probably also relates to pollution of the Baltica sector of Iapetus from the approaching Avalonia Plate. Patterns of evolutionary biodiversity and palaeobiogeographical linkages support the geochemical signatures in interpreting the tectonic history of the region. Extinction of lingulate brachiopod faunas in the Tremadoc, followed by subsequent recovery and emergence of benthic assemblages typical of the Ordovician Evolutionary Fauna in the Billingen–early Volkhov regional stages coincide with significant changes in geochemical characteristics of water masses across the Baltoscandian basin. The early and mid Ordovician (Arenig to Llandeilo) brachiopod faunas of the North Estonian Confacies Belt are characterized by high endemism and low turnover rates, whereas increased immigration resulted in the extinction of a number of local lineages in the late Llanvirn. From the mid Caradoc to mid Ashgill, when Baltica was drifting on a course to collide eventually with Avalonia and gradually approach Laurentia, brachiopod assemblages were characterized by higher turnover rates. At the same time they gradually became more cosmopolitan and less influenced by the invasion of new faunas.