Bivalves are filter feeders that can accumulate and concentrate waterborne contaminants present in the water in which they live. Biotoxins, pathogenic bacteria, viruses, and heavy metals present in the aquaculture environment constitute the main hazards for human health. The most common method employed for combating waterborne pollutants in bivalves is depuration with purified seawater. Although this method is effective at increasing the microbiological quality of bivalves, in most cases, it is ineffective at eliminating other risks, such as, for example, viruses or heavy metals. Biological (bacteriocins and bacteriophages), physical (UV light, ozone, and gamma-irradiation), chemical (metallothioneins and chitosan), and other industrial processing methods have been found to be useful for eliminating some contaminants from seawater. The aim of this work was to provide a review of academic articles concerning the use of treatments complementary to conventional depuration, aiming to improve depuration process efficiency by reducing depuration times and decreasing the levels of the most difficult-to-erase contaminants. We conclude that there are different lab-tested strategies that can reduce depuration times and increase the food safety of bivalve produce, with possible short- and long-term industrial applications that could improve the competitivity of the aquaculture industry.