The δ18O and δ13C values of brachiopod shell calcite are commonly used as proxies for ancient environmental marine conditions and secular changes in ancient ocean chemistry. The variability of δ18O and δ13C across modern shelf settings is, however, not well documented. This study presents δ18O and δ13C data from 407 Holocene (< 5000 yr BP) and living brachiopods collected from 220 sites across ∼ 3000 km along Australia’s southern shelf, the largest cool-water carbonate shelf in the modern world. Significant isotopic variability is present in separate specimens, at individual sites, and across the entire region. Individual specimens analyzed at multiple shell positions have an isotopic range of values up to 1.3‰ and 1.9‰ for δ18O and δ13C respectively. Multiple brachiopods at a single site have values that vary as much as 2.1‰ for δ18O and 1.8‰ for δ13C. Regional variability ranges on the order of 3.6‰ and 3.4‰, for δ18O and δ13C respectively. The distribution of intrasite variability can be divided into areas of high and low variability. Areas characterized by low variability occur in zones of relatively consistent shelf water conditions. High-variability zones usually correspond to areas of seasonal upwelling onto the shelf, and this aspect is interpreted to be the main cause of isotopic variability. Upwelling waters are cold, leading to higher δ18O values, and are commonly rich in respired dissolved inorganic carbon (DIC) and nutrients, promoting active phytoplankton growth and leading to variable δ13C values. The extensive spatial coverage across this vast latitude-parallel region provides a valuable baseline illustrating the isotopic range that could occur in a single layer in the rock record. Furthermore, changes in isotopic signatures measured across stratigraphy might not necessarily reflect secular changes in ocean chemistry but, instead, could be recording local changes in shelf circulation and upwelling intensity.