The quality of water from dental units is of considerable importance since patients and dental staff are regularly exposed to water and aerosols generated from the dental unit. This study analyzed the microbial quality of water obtained for periodical monitoring from 56 dental units in different dental practices in Hesse. Contamination by Legionella spp., Pseudomonas aeruginosa, and increased total colony counts were detected in 27.8%, 3.5%, and 17% of samples. Legionella pneumophila serogroup 1 accounted for 28% of Legionella isolates. The Legionella concentration was >100 cfu/100 ml in 84% of contaminated samples. Samples collected from an instrument channel were more frequently contaminated by Legionella than those from cup filler (41.7% vs. 18.6%, p = 0.02). After release of these results, decontamination measures were performed in units that had revealed unsatisfactory results. The outcome of the intervention was followed-up by microbiological analysis. At follow-up, 65.2% and 72.7% of waterlines that had previously been contaminated by Legionella or had shown increased total colony counts were free of contamination. Our results show a high rate of contamination of water from dental units in dental practices in Hesse. They highlight the risk of exposure for patients and personnel and the need for effective strategies to reduce microbial contamination.