In this study, we studied the levels of both of the main pigments in Salmonidae—astaxanthin (Ax) and canthaxanthin (Cx)—accumulated in the liver, female gonads, and male gonads of rainbow trout (Oncorhynchus mykiss) reared in water containing the fungicide mancozeb (MZ) in concentration levels permitted by European legislation. Experimental fish were divided into three groups: the first was a control group, the second was fed with market feed (containing Ax and Cx), and the third was fed with market feed (containing Ax and Cx) and reared in environmental water containing permissible MZ levels. The diet preparation followed the manufacturer’s recommendations. The accumulated pigment quantities were measured using an HPLC-PDA method after selective extraction: Ax ranged from 2.490 ± 0.247 mg/kg (female gonads, second group) to 0.176 ± 0.007 mg/kg (liver, control group), and Cx—from 2.406 ± 0.166 mg/kg (female gonads, second group) to 0.103 ± 0.010 mg/kg (liver, control group). The pattern of the accumulation of both pigments in the three organs in the specimens of the three groups was sustainable: the amount of Ax was always greater than that of Cx, and the correlation between their concentrations was very high. The pigments were accumulated most intensively in the female gonads, followed by the male gonads and the liver. This trend was confirmed for all three experimental groups. However, the differences in the last third group were very small, and the levels of the xanthophylls accumulated were the lowest. A particular cause of the latter findings was the ongoing detoxification reactions and the disposal of MZ, in which Ax and Cx were involved as antioxidants.