Due to agricultural runoff, pesticides end up in aquatic ecosystems and some accumulate in marine bivalves. As filter feeders, bivalves can accumulate high concentration of chemicals in their tissue representing a potential risk for the health of human and aquatic ecosystems. So far, most of the studies dealing with pesticides contamination in marine bivalves, for example, in the French Atlantic and English Channel coasts, have focused on old generation of pesticides. Only a few investigated the new emerging pesticides partly due to methodological challenges. A better understanding of the most sensitive and reliable methods is thus essential for accurately determining a wide variety of environmentally relevant pesticides in marine bivalves. The review highlighted the use of more environmentally friendly and efficient materials such as sorbents and the “Quick Easy Cheap Effective Rugged Safe” extraction procedure to extract pesticides from bivalve matrices, as they appeared to be the most efficient while being the safest. Moreover, this method combined with high-resolution mass spectrometry (MS) technique offers promising perspectives by highlighting a wide range of pesticides including those that are not usually sought. Finally, recent developments in the field of ultrahigh-performance liquid chromatography coupled to MS, such as two-dimensional chromatography and ion mobility spectrometry will improve the analysis of pesticides in complex matrices.