Digital holographic microscopy is suitable for the detection of microbial particles in a rapidly flowing fluid since in this technique the focusing can be carried out as post-processing of a single captured image. This image, known as a digital hologram, contains the full complex wave front information emanating from the object which forms an interference pattern with a known reference beam. Post-processing is computationally intense and it constitutes a bottleneck for real time inspection of fast moving scenes. In the current work, GPU computation is used to accelerate the post-processing of the holographic images captured by digital holographic microscopy. Efficiency and reliability of a pre-processing step in order to eliminate low information content holographic images is also investigated. Â© 2014 SPIE.