Acetylcholinesterase (AChE) activity was analyzed as a molecular marker indicative of exposure to organophosphorus pesticide residues in individuals of the endemic clam species Semele solida in selected coastal locations of Chile's VIII Region. AChE activity was assayed in clams from (i) Penco Beach near the mouth of the Andalién River (Concepción Bay), (ii) Lenga Beach, near the mouth of the Lenga Estuary (San Vicente Bay), and (iii) Coliumo Beach, near the mouth of the Coliumo Estuary (Coliumo Bay). We also analyzed variations in protein content of clam hemolymph, and variability in the activity of AChE in relation to the sizes of the individual clams sampled. Collection of the clams was done using routine methods, during the spring of 2005, the period during which the use of pesticides is typically intensified in the surrounding forestry and agriculture. The results showed no significant correlation of AChE activity with either the size of the clam, or with the concentration of proteins in the hemolymph. The lowest AChE activity was observed in clams from mouth of the Andalién River (187.5 ± 34.9 Umin−1) which was significantly less than that measured in specimens collected near the mouth of the Coliumo Estuary and the mouth of the Lenga Estuary. A very close relation was observed between the degree of anthropogenic inputs, ocean dynamics, and alterations in AChE activity in S. solida. This clam appears to be a useful indicator species, and AChE activity a sensitive marker for the presence of xenobiotics.