Carbonate minerals are a major reservoir in the global carbon cycle and a key player in the sequestration and emission of atmospheric CO2. In addition to the minerals’ frequent use in agriculture and construction, carbonate formation has been targeted for anthropogenic CO2 sequestration. Due to carbonate’s importance in geological and anthropogenic realms, research on carbonate characterization and quantification is of interest. Here, we demonstrate a method to identify and quantify calcite (CaCO3) and dolomite (CaMg(CO3)2) in sediment matrices using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). Needing only a few minutes per sample, DRIFTS is a rapid technique that does not require hazardous chemicals and does not destroy samples during analysis. We selected the 2515 ± 9 cm−1 absorbance bands for quantification as they exhibited little interference from sediment matrix minerals and large peak areas relative to other bands. The DRIFTS technique was compared to the traditional acidification headspace analysis method on artificial mixtures of sediment and carbonate as well as natural lake bed and river bank samples from the Upper Sangamon River Basin in Illinois, USA. DRIFTS offers an additional advantage over acidification in that it permits carbonate mineral identification simultaneously with its quantification. Though DRIFTS estimates were higher, a good correlation was found between DRIFTS and acidification estimates for both lake sediments (R2 = 0.99) and bank samples (R2 = 0.92), indicating DRIFTS is a reliable method for carbonate quantification in sediment matrices.