Bicarbonate salts are used in various industrial processes and could even serve as an alternative source of carbon in bioprocesses involving photosynthetic organisms. Industrial productions require efficient monitoring and control to ensure that their output will meet target specifications. To this end, a simple and rapid in situ quantification method was developed for bicarbonate, carbonate and phosphate ions using Attenuated Total Reflectance-Fourier Transform Infrared (ATR FT-IR) spectroscopy combined with partial least squares (PLS). The resulting multivariate approach allows the simultaneous determination of inorganic carbon and orthophosphate ions concentrations in aqueous solutions (R2 > 0.98, root-mean-square-errors of the cross validation RMSECV < 3.3%). Validation of the method was achieved through replicability and repeatability tests. Univariate calibration graphs are linear over a concentration range of 150 mM (R2 > 0.9990). Quantification limits for those ions were in the 6.9-17.2 mM range, as determined from univariate models. The multivariate model was successfully applied to a microalgal culture of Scenedesmus obliquus using bicarbonate as the carbon source and a phosphate buffer to maintain the pH. This analytical technique did not require extraction or chemical treatment and no sample preparation is needed. The results demonstrate the potential of ATR FT-IR method to study inorganic carbon and phosphate species during a bioprocess.