Microscopic analysis of micro particles in situ in diverse water environments is necessary for monitoring water quality and localizing contamination sources. Conventional sensors such as optical microscopes and fluorometers often require complex sample preparation, are restricted to small sample volumes, and are unable to simultaneously capture all pertinent details of a sample such as particle size, shape, concentration, and three dimensional motion. In this article we propose a novel and cost-effective robotic system for mobile microscopic analysis of particles in situ at various depths which are fully controlled by the robot system itself. A miniature underwater digital in-line holographic microscope (DIHM) performs high resolution imaging of microparticles (e.g., algae cells, plastic debris, sediments) while movement allows measurement of particle distributions covering a large area of water. The main contribution of this work is the creation of a low-cost, comprehensive, and small underwater robotic holographic microscope that can assist in a variety of tasks in environmental monitoring and overall assessment of water quality such as contaminant detection and localization. The resulting system provides some unique capabilities such as expanded and systematic coverage of large bodies of water at a low cost. Several challenges such as the trade-off between image quality and cost are addressed to satisfy the aforementioned goals.