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Sources for contamination in breweries can occur as "primary" contaminations (yeast pitching, and brewhouse related contaminations), or as "secondary" contaminations (packaging and cellaring), as well as in tap systems. They are usually not sudden occurrences, but a result of continued growth of microorganisms in a problem area. Historically, re-pitching yeast was often a source of contamination, however, more recently this has become less of a source for contaminations due to better education and techniques. Typical sources for contamination also include unclean equipment such as thermometers, manometers, valves, dead ends, gas pipes, leaks in any part of the system (especially at heat exchangers), wort aeration equipment, and even worn floor surfaces. More than half of documented contaminations come from the packaging system. These are typically the sealer (35%), the filler (25%), the bottle inspector (10%), dripping water from the bottle washer (10%), and the environment close to the filler and sealer (10%). In regards to the environment as a source of contamination, this has been found to be from airborne contaminants near the filler and crowner. The higher the humidity and the more airflow, the more chances of airborne contamination. In tap systems at taverns, 'one-way' valves that are attached to kegs have been found to be a source of contamination, as well as the dispensing line <ref name="storgards_2000" />.
Bokulich et al. (2015) studied the microbial populations throughout a brewery (presumably Allagash) that produces clean beer, mixed fermentation sour beer, and spontaneously fermented coolship ale. They found that most of the microbes living in breweries were introduced from the ingredients such as malted barley and hops, and many populations were confined to specific rooms or areas within the brewery. Some species did spread to other rooms. Beer resistant lactic acid bacteria spread throughout the brewery (although more abundantly found near packaging equipment and fermenters that were filled with sour beer), but the clean beer was largely uncontaminated. Ale yeast was found throughout the brewery, especially in the fermentation cellar. Malted grains were determined to be the highest source of potentially contaminating microbes in the hotside areas of the brewery compared to other microbe sources such as human skin, outdoor air, soil, saliva, feces, water from the plumbing, etc. Hops were determined to be the highest source of microbes in the cellar fermentation areas, and yeast was the highest population in fermenter and packaging areas. While human skin was a minor contributor to microbe populations found in the brewery, oak barrel surfaces were populated with microbes from unknown sources. Therefore, it was determined in this study that raw materials are the major source for potential contaminants in a brewery, although minor sources such as sinks are still potential problems. Seasonality played a minor role in the populations of microbes throughout the brewery, with ale yeast and ''Candida santamariae'' spreading from the fermentation and packaging area to the rest of the brewery from fall to summer (it was proposed that the warming from fall to summer played a role in the spread of ale yeast and ''Candida santamariae'' throughout the brewery). ''Micrococcus'' and ''Kocuria'' were found in more localized areas such as the floors and other surfaces in the barrel room, cellar, and packaging room. ''Acetobacter'' and ''Lactobacillus'' were found specifically in areas where a lot of wort or beer was being processed (conveyor belts and floors below the packaging equipment, hotside and cellar area sinks, and sample ports on kegs and fermenters).
===Biofilms===