Simultaneous application of polarization microscopy and dark field techniques has been used to study the internal structure of microbial cells. The dark field technique displays subtle cell structures like glowing objects on a dark background. In the polarizing microscope, cross polarizing filters along with the first-order quartz compensator and a rotary table show the maximum birefringence of the individual structures. The material containing microorganisms was collected in the villages of Sýkořice and Zbečno (Křivoklátsko Protected Landscape Area). The objects were studied in a laboratory microscope Carl Zeiss Jena type NfpK equipped with In Ph 160 basic body with variable dark field, special condenser with interchangeable diaphragm apertures, a rotary table, Meopta Praha polarizer, analyzer, first-order quartz compensator from LOMO Sankt Petersburg, and a digital Nikon D 70 DSLR camera. Three orders of microorganisms were studied: Siphonocladales, Chlorococcales, and Peritricha. Anisotropic structures in different amounts and sizes (e.g., granules and microfibrils) or in different configurations (e.g., cell walls or pellicle) have been found in all Protista organisms under study. Filamentous algae of the genus Cladophora (Cladophoraceae, Siphonocladales, Ulvophyceae) featured a strongly birefringent cell wall (shape birefringence) surrounded by less birefringent periphyton (microbial biofilm), at the edges of which cyanobacterial fibers could be recognized—a very important finding. The coccal algae of the genus Scenedesmus (Scenedesmataceae, Chlorococcales, Chlorophyceae) exhibited not only strongly birefringent granules, but also strongly birefringent microfibrils in the cytoplasm outside the strongly birefringent cell walls—very important finding. Of all the studied microorganisms, the weakest birefringence was shown in the surface membrane (pellicle) of the Vorticella (Vorticellidae, Peritricha, Ciliata). On the other hand, the ring of cilia on the top of the body had a somewhat stronger birefringence—an important finding. In conclusion, the dark field technique provides a high contrast image in the microscope and, if supplemented simultaneously by polarization microscopy, will allow us to partially infer the composition of the examined structures.