Results showed that 75% of the analyzed samples in a drinking water network were positive for fungi, in a range of 1–3,000 CFU/mL. Identification resulted in nine species of fungi and four species of yeasts being listed: Bjerkandera, Penicillium, Paraconiothyrium, Paecilomyces, Debaryomyces, Rhodotorula and Cryptococcus. Although yeasts showed higher traceability than filamentous fungi, the fungal genus Penicillium had relevance by both traceability (six species) and its role in mycotoxin generation. From volatile organic compound (VOC) mycotoxins and extracts analysis from P. ochrochloron and P. purpurogenum water–M9 culture, six groups were identified: phenols, alcohols, alkenes, monoterpenes, aldehydes and alkanes, phenols being the predominant group (2,4-bis(1,1-dimethyl)phenol 40–88%). P. ochrochloron water culture and M9 culture reported signals of toxicity: the first one as genotoxic for 0.5 y 1 mg/mL mycotoxin extract and the second one as cytotoxic. M9 media promoted a higher number of compounds in both species and a decrease in phenol predominance in P. ochrochloron but not in P. Purpurogenum. The results showed Penicillium and Debaryomyces as prevalent filamentous fungi and yeast in assessed networks, suggesting that these could be indicators of fungi and yeast presence in drinking water systems.