The sedimentary record of carbonate carbon isotopes (δ13Ccarb) provides one of the best methods for correlating marine strata and understanding the long-term evolution of the global carbon cycle. This work focuses on the Late Ordovician Guttenberg isotopic carbon excursion, a ca 2·5‰ positive δ13Ccarb excursion that is found in strata globally. Substantial variability in the apparent magnitude and stratigraphic morphology of the Guttenberg excursion at different localities has hampered high-resolution correlations and led to divergent reconstructions of ocean chemistry and the biogeochemical carbon cycle. This work investigates the magnitude, spatial scale and sources of isotopic variability of the Guttenberg excursion in two sections from Missouri, USA. Centimetre-scale isotope transects revealed variations in δ13Ccarb and δ18Ocarb greater than 2‰ across individual beds. Linear δ13Ccarb to δ18Ocarb mixing lines, together with petrographic and elemental abundance data, demonstrate that much of the isotopic scatter in single beds is due to mixing of isotopically distinct components. These patterns facilitated objective sample screening to determine the ‘least-altered’ data. A δ18Ocarb filter based on empirical δ18Ocarb values of well-preserved carbonate mudstones allowed further sample discrimination. The resulting ‘least-altered’ δ13Ccarb profile improves the understanding of regional as well as continental-scale stratigraphic relations in this interval. Correlations with other Laurentian sections strongly suggest that: (i) small-scale variability in Guttenberg excursion δ13Ccarb values may result in part from local diagenetic overprinting; (ii) peak-Guttenberg excursion δ13Ccarb values of the Midcontinent are not distinct from their Taconic equivalents; and (iii) no primary continental-scale spatial gradient in δ13Ccarb (for example, arising from chemically distinct ‘aquafacies’) is required during Guttenberg excursion-time. This study demonstrates the importance of detailed petrographic and geochemical screening of samples to be used for δ13Ccarb chemostratigraphy and for enhancing understanding of epeiric ocean chemistry.