The objective of this work was to discover a biochemical pathway to explain the transfer of cadmium, a toxic element, from seawater to cultured mussels. Understanding the intricacies of this transfer is crucial for global mussel crops, as it has the potential to mitigate risks to human health and prevent economic losses in the industry. We focused our investigation on Yal Bay, a typical area with intense mussel aquaculture activity (16,000 t y−1) in the inland sea of southern Chile. Seasonal samples of blue mussels (Mytilus chilensis) were collected and analyzed from September 2014 to December 2015 at two integrated depths (0–5 m and 5–10 m). Diurnal and nocturnal seston, seawater, benthic sediments and decanted suspensions from the water column were recorded. Our findings indicate that nocturnal seston satisfactorily explains the presence of cadmium in Mytilus chilensis aquaculture throughout its annual temporal distribution (Spearman rs = 0.63, p = 0.002).