Endotoxins are pyrogenic lipopolysaccharides from Gram-negative bacteria that are known to induce fever, septic shock, and multiple organ failure, posing a substantial risk to human health. Drinking water systems are especially prone to home microbiomes containing a large variety of Gram-negative bacteria. Consumption of water from these systems in developed countries is generally regarded as non-hazardous to humans due to the low number of non-pathogenic bacterial cells per milliliter and oral admission. To assess potential risks posed by endotoxins in drinking water systems, we conducted a conventional microbiological investigation on a local community water system in the north of Germany and mined the resulting data to investigate the endotoxin contents of some of the most abundant microbiota found during these analyses. Using a Limulus amoebocyte lysate (LAL) -based endotoxin detection method, average normalized endotoxin content was determined. Although the average culturable amounts of microbiota in the drinking water system were insufficient to exert endotoxin levels critical to human health, peaks and acute contaminations may pose substantial health risks.