Lake Chapala is the largest natural freshwater reservoir in Mexico and the third largest lake in Latin America. Lakes are often considered the final deposit of polluting materials; they can be concentrated in the organisms that inhabit them, the water, and the sediments. The PCBs and PBDEs are environmental pollutants highly studied for their known carcinogenic and mutagenic effects. PCB and PBDE bioaccumulation levels were determined in Chirostoma spp., Cyprinus carpio, and Oreochromis aureus. In addition, we monitored the concentrations of PCBs and PBDEs in sediment and water from Lake Chapala were monitored. Samples were collected during two periods, in October 2018 and May 2019. The samples were analyzed by gas chromatography coupled with mass spectrometry. Two bioaccumulation factors were determined in fish, one in relation to the concentration of PCBs and PBDEs in sediments and the other in relation to the concentration of PCBs and PBDEs in water. The PCB levels were 0.55–3.29 ng/g dry weight (dw) in sediments, 1.43–2.98 ng/mL in water, 0.30–5.31 ng/g dw in Chirostoma spp., 1.06–6.07 ng/g dw in Cyprinus carpio, and 0.55–7.20 ng/g dw in Oreochromis aureus. The levels of PBDEs were 0.17–0.35 ng/g dw in sediments, 0.13–0.32 ng/mL in water, 0.01–0.23 ng/g dw in Chirostoma spp., 0–0.31 ng/g dw in Cyprinus carpio, and 0.1–0.22 ng/g dw in Oreochromis aureus. This study provides information for a better understanding of the movement, global distribution, and bioaccumulation of PCBs and PBDEs. The results show that the fish, water, and sediments of Lake Chapala are potential risks to the biota and the local human population.