Nontuberculous mycobacteria (NTM) are opportunistic pathogens found in natural and human-engineered waters. In 2009, a relative increase in the isolation of Mycobacterium gordonae from pulmonary samples originating from General Hospital Zabok was noted by the National Mycobacteria Reference Laboratory. An epidemiological survey revealed a contamination of the cold tap water with M. gordonae and guidelines regarding sputum sample taking were issued. In addition, all incident cases of respiratory infection due to NTM reported from 2007 to 2012 at General Hospital Zabok were included in a retrospective review. Out of 150 individual NTM isolates, M. gordonae was the most frequently isolated species (n = 135; 90%) and none of the cases met the criteria of the American Thoracic Society for pulmonary NTM disease. While concomitant Mycobacterium tuberculosis infection was confirmed in only 6 (4%) patients, anti-tuberculosis treatment was initiated for a significant portion of patients (n = 64; 42.6%) and unnecessary contact tracing was performed. This study points out the need to enhance the knowledge about NTM in our country and indicates the importance of faster NTM identification, as well as the importance of good communication between laboratory personnel and physicians when evaluating the significance of the isolated NTM.