The study of intracellular water in living cells is a challenge of fundamental importance. While the critical roles of water in maintaining and propagating life have been widely recognized and accepted, our understanding of water/biomolecule interactions is surprisingly limited. Using Raman microspectroscopic imaging of a living yeast cell followed by a multivariate analysis in form of the nonnegative matrix factorization method, we successfully resolve organelle-specific water structures. The intensities and the band profiles of the segregated water OH stretch spectra yield important and otherwise unobtainable information on the extensive effect of the water/biomolecule interactions in a given organelle on the hydrogen-bonding network of water molecules. Copyright © 2012 John Wiley & Sons, Ltd.