The extensive use of fungicides causes their continuous release into the environment through spraying, soil seepage, leaching, and runoff. It has been observed that their residues can be found in foods and a variety of environmental compartments, such as wastewater, lakes, rivers, sediments, drinking water sources (groundwater and surface water), treated water, and drinking water. A sensitive GC-MS/MS, using dynamic multiple reaction monitoring, an analytical method was developed to determine 10 fungicides (azoxystrobin, boscalid, captan, cyproconazole, cyprodinil, hexaconazole, metalaxyl, myclobutanil, paclobutrazol, and prochloraz) in drinking water. A solid-phase extraction method for sample preparations and validations was performed according to SANTE 2019 guidelines. All fungicides demonstrated mild or medium matrix effects (ME) ranging from 40.1% to 11.2%. Their recoveries ranged between 60% and 110%. The limits of detection were equal to or higher than 0.01 μg/L. The method was employed on 18 drinking water samples collected from public taps in Northern Evros, Greece, distributed in six sampling sites. Azoxystrobin, boscalid, cyproconazole, cypronidil, metalaxyl, and paclobutrazol mean concentrations did not surpass the allowable limit of 0.1 μg/L set by EU in any sampling site. Hexaconazole mean concentrations were higher than 0.1 μg/L in one sampling site, while prochloraz mean concentration showed limit exceedances in all sampling sites. Captan was not detected in any sampling site, and myclobutanil mean concentrations demonstrated exceedances of the permissible limit in four sampling sites. The presence of fungicide residues in the studied area is mainly due to the occasional point-sources pollution and preferential flow. Additionally, through the use of water, the risk of pesticides to human health was assessed for two different age groups. The sum of the hazard quotient values in each of the studied drinking water was less than unity. Consequently, the acute risk assessment procedure regards the examined drinking water as safe. Nevertheless, as prochloraz carcinogenic risk values were higher than the safe limit suggested by USEPA for both age groups, the existence of prochloraz residues raises concerns about chronic toxicity.