Numerous anthropogenic and natural particle contaminants exist in diverse aquatic systems, with widely unknown environmental fates. We coupled a flow tube with a digital in-line holographic microscopy (nano-DIHM) technique for aquatic matrices, for in situ real-time analysis of particle size, shape, and phase. Nano-DIHM enables 4D tracking of particles in water and their transformations in three-dimensional space. We demonstrate that nano-DIHM can be automated to detect and track oil spills/oil droplets in dynamic systems. We provide evidence that nano-DIHM can detect the MS2 bacteriophage as a representative biological-viral material and mercury-containing particles alongside other heavy metals as common toxic contaminants. Nano-DIHM shows the capability of observation of combined materials in water, characterizing the interactions of various particles in mixtures, and particles with different coatings in a suspension. The observed sizes of the particles and droplets ranged from ∼1 to 200 μm. We herein demonstrate the ability of nano-DIHM to characterize and distinguish particle-based contaminants in water and their interactions in both stationary and dynamic modes with a 62.5 millisecond time resolution. The fully automated software for dynamic and real-time detection of contaminants will be of global significance. A comparison is also made between nano-DIHM and established techniques such as S/TEM for their different capabilities. Nano-DIHM can provide a range of physicochemical information in stationary and dynamic modes, allowing life cycle analysis of diverse particle contaminants in different aquatic systems, and serve as an effective tool for rapid response for spills and remediation of natural waters.