The purpose of this study was to identify the prevalence of fungal colonization in water systems and to evaluate the effect of decreasing fungal colonization by a copper-silver ionization system. Environmental samples were collected for fungal culture prospectively during a 1-year period (2011-2012) at the study hospital. A total of 392 water samples were examined from five buildings on March 1, 2011 and February 29, 2012. Fungi were isolated in 13 (3.4%) of 392 water samples from five buildings. The prevalence of fungal colonization in buildings was decreased from 4.76% (9/189) to 1.97% (4/203), a reduction of more than 40%, in pre-ionization and post-ionization treatment (p < 0.001). Thirteen (3.4%) of 392 water samples yielded fungi including Fusarium species (n = 7), Penicillium species (n = 2), Scedosporium species (n = 2), Aspergillus species (n = 1), and one unidentifiable mold. The number of isolated Fusarium species in ionized water samples (0.5% (1/203)) was statistically lower than those in nonionized (3.2% (6/189)) (p = 0.003). Our finding may determine if this ionization method can be applied for control of waterborne fungi colonization in hospital water systems.