The Niobrara Formation of north‐east Colorado, USA, has anomalously negative δ18O values compared to all other Cretaceous chalks. These unique δ18O values have been attributed to elevated heat flow and/or freshening of the Cretaceous Western Interior Seaway. This work utilises clumped isotopes of calcite (Δ47), peak burial temperatures estimated from pyrolysis data, and strontium and neodymium isotopes of carbonate to re‐evaluate the origin of the calcite's 18O‐depletion. Peak temperatures indicate lateral variability in geothermal gradients of ca 20°C/km at the tens of kilometre scale, and corroborate prior studies proposing locally elevated palaeotemperatures. Greater insight is provided by numerical models of calcite recrystallisation and oxygen isotope evolution that are constrained by measured Δ47‐derived temperatures, calcite δ18O values and inferences from the 87Sr/86Sr and εNd values. The models indicate that (1) sea water in the seaway had normal marine δ18O values of −1 (VSMOW) except on the eastern margin of the basin where some freshwater dilution yielded −2 to −3‰ (VSMOW) water, and (2) the main driver of the anonymously negative calcite δ18O values was a semi‐open hydrologic system that provided a few percent by pore volume of meteoric groundwater derived from post‐Laramide recharge into the basin. Minor contributions were a Laramide‐aged heat pulse related to the underlying Colorado Mineral Belt, the thermal insulating effects of now eroded coals, and a small flux of compaction‐driven Cretaceous sea water evolved by smectite dehydration. However, those three factors alone were insufficient drivers of the calcites' 18O depletion. High burial temperatures are interpreted to have caused clumped isotope reordering in at least one well, but those temperatures cannot yield the observed calcite δ18O values. The study illustrates the unique attributes of the Niobrara's diagenetic system that results in its anomalous δ18O values, and reaffirms the value of clumped isotopes in unravelling the diagenetic history of chalk systems.