The structure of trifluoroacetylacetone in argon and nitrogen matrices and association with water molecules were studied by the means of Fourier transform infrared absorption spectroscopy (FTIR) aided with density functional theory (DFT) calculations. The absorption bands of trifluoroacetylacetone isolated in argon can be attributed to the single conformer 1,1,1-trifluoro-4-hydroxy-3-penten-2-one [AcAcF3(CO)] which is in good agreement with previous studies. Absorption bands of trifluoroacetylacetone isolated in nitrogen matrix cannot be explained by the presence of only one conformer and with the aid of DFT calculations both conformers 1,1,1-trifluoro-4-hydroxy-3-penten-2-one and 5,5,5-trifluoro-4-hydroxy-3-penten-2-one [AcAcF3(OH)] are confirmed to coexist in the nitrogen matrix. Addition of water to the trifluoroacetylacetone–matrix mixture resulted in appearance of new spectral bands not belonging either to trifluoroacetylacetone or water monomers confirming the formation of trifluoroacetylacetone–water complexes. The most abundant isomer out of trifluoroacetylacetone–water complexes was found to be the one formed from 5,5,5-trifluoro-4-hydroxy-3-penten-2-one and water attached to its C=O group in both matrices, the other one isomer of 1,1,1-trifluoro-4-hydroxy-3-penten-2-one–water complex is also observed in smaller amounts.