Tufa deposits are potential terrestrial archives of palaeoenvironmental and palaeoclimatic information. This study assesses the potential of stable isotopic archives from two closely juxtaposed Holocene tufa sites in SE Spain. The Ruidera site contains deep‐water lacustrine micrites and tufas, whereas the nearby Alcaraz site represents a shallow barrage tufa. Understanding site characteristics is critical to interpreting the stable isotopic variations. These Holocene lacustrine micrites have isotopic compositions consistent with modern European lake shore microbial carbonates, where the isotopic chemistry is strongly influenced by hydrological and residence time effects. All the lacustrine micrite δ^13^C values were influenced by microenvironmental microbial effects to some degree. Because of these effects, stable isotope data from lacustrine microbial micrites and tufas will not normally yield precise information on the isotopic composition of palaeoprecipitation, temperature or vegetation composition of an area. In contrast, Holocene tufas that formed in shallow, fast‐flowing riverine settings may contain valuable palaeoclimatic archives. The tufa deposits must be largely autochthonous, as at Alcaraz, where in situ reed stem encrustations are present. Records of relative change in air temperature and changes in the source of airmasses are potentially resolvable in the δ^18^O data. These interpretations can be verified by other independent climatic data where chronology is constrained. Variations in riverine tufa δ^13^C values probably record changes in local vegetation and/or soil respiration. Covariation between δ^18^O and δ^13^C values may be intrinsically linked to climatic factors such as aridity. Tentative palaeoclimatic interpretations for the middle Holocene at Alcaraz based on the isotope data suggest warming (or increasing influence of Mediterranean‐sourced precipitation) between approximately 5000–3000 radiocarbon years BP, accompanied by increased aridity. These interpretations are consistent with the sparse independent palaeoclimatic data and climate modelling results for the Holocene of SE Spain. This study supports the growing evidence that well‐chosen tufa sites could yield valuable palaeoclimatic information.