The microbial contamination of water miscible metalworking fluids (MWFs) is a serious problem in metal industry. A good maintenance of MWF re-circulation systems can extend the lifetime of coolants and ensure the quality of the tools produced. In MWFs, as in the other water-based environments, microorganisms usually live in the form of biofilms, the communities of bacteria and fungi attached to the surface of sumps, metal parts and also to each other. Biofilms exhibit very high resistance to biocides. The effect of biocides that are used as additives to MWFs to control the growth of the bacterial and fungal microbiomes (microorganisms characteristic to the individual coolant system) have become the subject of research only in recent years. There are also only sparse reports on the impact of biocides on microorganisms growing in biofilms in MWF installations. Fast growing mycobacteria are important members of these biofilm communities. Their presence has recently been linked with the occurrence of cases of hypersensitivity pneumonitis, a serious respiratory disorder in the metal industry employees. The new, relatively fast and inexpensive techniques to assess the species diversity within MWF microbiomes and their population size should be developed in order to control the microorganisms' proliferation in MWFs and to diminish the occupational exposure to harmful bioaerosols in metal industry.