Analysis of concentrations and biotoxicity of Cd, Pb and Zn in the coastal waters of Pagadian Bay is the primary focus of this study. A comparison was made between concentrations of the three heavy metals in seawater and in tissues of a molluscan species Lingula sp. in three stations over three sampling periods using the Atomic Absorption Spectrophotometer (AAS). Analysis from the AAS, revealed presence of lead and zinc while it gave negative results for cadmium. Tissue samples were found to contain more heavy metal concentrations than seawater which implies the abundance of heavy metals in the tissues of Lingula sp. Among the three stations, station 3 (Barangay Bomba) contained the highest concentration of lead and zinc while station 1 (Barangay Moricay) was found to contain the lowest concentration of the same heavy metal both for water and tissue samples. Results obtained from lead analysis exceed the permissible concentration of lead under American Standard which is 0.05ppm while values obtained from zinc analysis is within the range of the permissible concentration which is 5ppm as set by Environmental Protection Agency. Toxicity of the three heavy metals was also determined by obtaining its lethal concentration values using probit method. Lethal Concentration (LC50) values at 72 hours gave the following concentration values: 33.81ppm Cd, 184.68ppm Pb and 29.37ppm Zn . LC50 values of three heavy metals varied with respect to test concentration at a given exposure time.