The transition from the Proterozoic to the Phanerozoic Eon was accompanied by the rise of metazoan life, a key and unique biogeochemical milestone in Earth's history. Concomitant continental re-organization and collision were associated with enhanced continental reworking and changes in global ocean currents, with profound impacts on continental weathering rates, riverine run-off and associated changes in the ocean nutrient budget. The causal relationship between the geological re-organisation of continents and the biologic evolution of marine life, however, remains elusive. In this study, we investigate phosphatic shallow-water sedimentary successions from Kazakhstan, which host key marker horizons from the Precambrian-Cambrian (Pc-C) boundary. We show that a rapid change (over ca. 3 Myrs) towards heavier stable Mg isotope compositions of the phosphatic sedimentary deposits in Kazakhstan, which we consider representative for contemporaneous ocean chemistry, co-varies with changes in radiogenic Sr isotope signatures. We propose that ocean chemistry at the Pc-C boundary, represented through this co-variation, was strongly affected by continental re-organization and associated weathering, which, in analogy, would have affected ocean nutrient levels. A rapid reversal of isotope compositions towards signatures similar to those prior to the isotope excursion likely reflects the fading influence of weathering and a buffering of water-rock interactions during oceanic spreading. We conclude that, based on the positive, coupled 87Sr/86Sr- δ26Mg isotope spike in ocean water chemistry, a link between Gondwana re-organization at the Pc-C boundary and the marked change in marine fauna seems plausible.