Pharmaceutical water is the most widely used raw material and solvent in the process of pharmaceutical products, which is widely used in the cleaning and disinfecting process of appliances, equipment, facilities and systems, and is involved in the whole process of pharmaceutical products. Pharmaceutical water is one of the main sources of microbial contamination of pharmaceutical products, so the microbial safety of pharmaceutical water is crucial for pharmaceutical quality. This paper mainly introduces the characterization of the pharmaceutical water system, and conducts biofilm analysis. Due to the characteristics of oligotrophic and slow-growing of microorganisms in the pharmaceutical water system, this paper also further discusses the microbiological testing and culture methods of pharmaceutical water, so as to provide reference for the establishment of a scientific and reasonable microbiological testing system, as well as provide an important theoretical basis and new ideas for further research on hard-to-culture microorganisms.