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ABSTRACT Carbonate rocks and natural waters exhibit a wide range in the concentration and isotopic composition of strontium. This wide range and the quantifiable covariation of these parameters can provide diagnostic tools for understanding processes of fluid‐rock interaction. Careful consideration of the uncertainties associated with trace element partitioning, sample heterogeneity and fluid‐rock interaction mechanisms is required to advance the application of the trace element and isotope geochemistry of strontium to studies of diagenesis, goundwater evolution, ancient seawater chemistry and isotope stratigraphy. A principal uncertainty involved in the application of Sr concentration variations to carbonate systems is the large range of experimental and empirical results for trace element partitioning of Sr between mineral and solution. This variation may be a function of precipitation rate, mineral stoichiometry, crystal growth mechanism, fluid composition and temperature. Calcite and dolomite in ancient limestones commonly have significantly lower Sr concentrations (20–70 p.p.m.) than would be expected from published trace element distribution coefficient values and Sr/Ca ratios of most modern sedimentary pore waters. This discrepancy probably reflects the uncertainties associated with determining distribution coefficient values. As techniques improve for the analytical measurement and theoretical modelling of Sr concentration and isotopic variations, the petrological analysis of carbonate samples becomes increasingly important. The presence of even small percentages of non‐carbonate phases with high Rb concentrations and high 87 Sr 86 Sr values, such as clay minerals, can have significant effects on the measured 87 Sr/ 86 Sr values of carbonate rocks, due to the decay of 87 Rb to 87 Sr. For example, a Permian marine limestone with 50 p.p.m. Sr and 1 p.p.m. Rb will have a present‐day 87 Sr/ 86 Sr value that is >2 × 10 −4 higher than its original value. This difference is an order of magnitude greater than the analytical uncertainty, and illustrates the importance of assessing the need for and accuracy of such corrections. A quantitative evaluation of the effects of water‐rock interaction on Sr concentrations and isotope compositions in carbonates strengthens the application of these geochemical tracers. Geochemical modelling that combines the use of trace elements and isotopes can be used to distinguish between different mechanisms of water‐rock interaction, including diffusive and advective transport of diagenetic constituents in meteoric pore fluids during the recrystallization of carbonate minerals. Quantitative modelling may also be used to construct diagnostic fluid‐rock interaction trends that are independent of distribution coefficient values, and to distinguish between mixing of mineral end‐members and fluid‐rock interaction.