We introduce a color digital holographic microscope for measuring the biological content of water samples. Our approach uses single shot RGB exposure in an in-line holographic setup to obtain color images. With the application of appropriate numerical algorithms we can fulfill color crosstalk compensation, segmentation, and twin image removal tasks, and we obtain good quality color image reconstructions with 1μm resolution from a 1mm3 volume. We briefly compare the conventional color CCD/CMOS and the Foveon X3 sensor for color digital holographic applications. The in-line holographic setup and reconstruction algorithms are presented with demonstrative simulations, experimentally captured and numerically reconstructed images.© (2010) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.