Heavy metals have been implicated as Lagoon pollutants from sources such as agriculture, mining and manufacturing industries and waste water treatment works. A study was carried out in the University of Lagos lagoon to investigate the seasonal bioavailability of the heavy metal contaminants Cd, Cr, Cu, Pb and Zn. The physical parameters pH, redox potential, temperature, TDS and conductivity were measured on site. Dried sediment samples were extracted using the Community Bureau of Reference (BCR) sequential procedure and analysed by ICP-OES. A certified reference material (CRM), BCR 701 (lake sediment) was used for quality assurance with recoveries ranging between 80-120%. Statistical analysis (ANOVA) showed that there was a significant difference between metal distribution in the dry and wet seasons. Cu, Pb and Zn were in the available fractions (carbonate, Fe/Mn oxide and organic). Cu was highest in the Fe/Mn oxide and organic fractions. This indicated that an increase in organic matter and reducing agents will avail the Cu. Zn was distributed in all fractions while Pb was found in the Fe/Mn oxide fraction (3.93- 21.3 %). Results showed that the bioavailability of Cu, Pb and Zn was high. Metal bioavailability by BCR indicates a potential risk of pollution in lagoon sediments as the available metals exceeded the permissible Sediment Quality Assessment Guidelines (SQAG’s) from Environmental Protection Agency (EPA).