The asymmetric unit of the title compound, C(16)H(12)ClF(3)N(2)O(3)S·H(2)O, contains two crystallographically independent organic mol-ecules and two water mol-ecules. The organic species are linked by an inter-molecular O-H⋯O hydrogen bond, while the water mol-ecules are connected to them through inter-molecular O-H⋯N hydrogen bonds. The thio-phene and phenyl rings are oriented at dihedral angles of 62.35 (4) in the first independent mol-ecule and 60.74 (5)° in the second, while the pyrimidine rings adopt twisted conformations in both molecules. Intra-molecular N-H⋯F inter-actions result in the formation of two five-membered rings having envelope conformations. In the crystal structure, further inter-molecular O-H⋯O and N-H⋯O hydrogen bonds link the mol-ecules into chains.