Ologe and Badagry Lagoons are important tropical lagoons in Lagos, Nigeria. The water quality and heavy metal concentration were studied for a period of 2 years (Aug. 2016 to Jul. 2018) using standard methods. The least temperature obtained was 28.70±0.05 C in Ologe Lagoon during the wet season and the maximum recorded was 29.41±0.08 in in Badagry Lagoon during the dry season. During the wet season (May-October) the temperature was steady and similar between the two connecting tropical lagoons. The salinity values vary at different stations in both Lagoon, 0.06 to 0.44% in Ologe Lagoon and 0.08 to 0.28% in Badagry Lagoon. Badagry Lagoon showed significant higher values in conductivity, total dissolved solid, chemical oxygen demand, biological oxygen demand, total suspended solid and total hardness across seasons. Heavy metal results showed that except for lead (0.25±0.10 mg/L), Ologe Lagoon had higher concentrations of all examined heavy metals (Zinc, copper, iron, chromium, lead, cadmium, manganese and cobalt) than Badagry Lagoon across season. Furthermore, cadmium, manganese and cobalt were not detected in Badagry Lagoon across season. The two studied connecting Lagoons especially Ologe Lagoon is exposed to dramatic deterioration in its water quality due to different wastes that discharge into the water body. These lagoons are clearly polluted by metals for various utilizations. As a result, the study suggests enforcing the controls on waste discharged into lagoons.