The Cellular Sensory and Optical Wave Computing Laboratory  in cooperation with the Waterworks of Budapest has developed an in-line digital holographic microscope that is able to count and classify small objects floating within water samples. Due to the applied holographic technology it is able to digitally reconstruct all the objects within a relatively large volume of water (1mm3, 100 times more than conventional microscopes). Using a special illumination of three wavelengths our device is able to color hologram reconstructions with 1 µm resolution and due to the sophisticated GPU implementation of the algorithms close to real time processing is achievable. The device is programmed color and shape based detection, classification and counting of different kind of algae in fluid samples. This way provides a really efficient water inspection system for water safety, environment monitoring and ecology applications.