The Yangibana rare earth element (REE) district consists of multiple mineral deposits/prospects hosted within the Mesoproterozoic Gifford Creek Carbonatite Complex (GCCC), Western Australia, which comprises a range of rock types including calcite carbonatite, dolomite carbonatite, ankerite–siderite carbonatite, magnetite–biotite dykes, silica-rich alkaline veins, fenite, glimmerites and what have historically been called “ironstones”. The dykes/sills were emplaced during a period of extension and/or transtension, likely utilising existing structures. The Yangibana REE deposits/prospects are located along many of these structures, particularly along the prominent Bald Hill Lineament. The primary ore mineral at Yangibana is monazite, which is contained within ankerite–siderite carbonatite, magnetite–biotite dykes and ironstone units. The ironstones comprise boxwork-textured Fe oxides/hydroxides, quartz, chalcedony and minor monazite and subordinate rhabdophane. Carbonate mineral-shaped cavities in ironstone, fenite and glimmerite alteration mantling the ironstone units, and ankerite–siderite carbonatite dykes altering to ironstone-like assemblages in drill core indicate that the ironstones are derived from ankerite–siderite carbonatite. This premise is further supported by similar bulk–rock Nd isotope composition of ironstone and other alkaline igneous rocks of the GCCC. Mass balance evaluation shows that the ironstones can be derived from the ankerite–siderite carbonatites via significant mass removal, which has resulted in passive REE concentration by ~ 2 to ~ 10 times. This mass removal and ore tenor upgrade is attributed to extensive carbonate breakdown and weathering of ankerite–siderite carbonatite by near-surface meteoric water. Monazite from the ironstones has strong positive and negative correlations between Pr and Nd, and Nd and La, respectively. These relationships are reflected in the bulk–rock drill assays, which display substantial variation in the La/Nd throughout the GCCC. The changes in La/Nd are attributed to variations in primary magmatic composition, shifts in the magmatic-hydrothermal systems related to CO2 versus water-dominated fluid phases, and changes in temperature.