Algal pigments areuseful in the estimation of primary production and phytoplankton biomass. Chlorophyll a, chlorophyll b and phaeophytina are notable algal pigments in this regard. Open lagoon are coastal environments known to exhibit continuous environmental gradients daily and seasonally. Algal pigments and environmental variables of the western parts of the Lagos Lagoon were investigated for six month at seven stations (November, 2015 April, 2016). The environmental indices reflected seasonal changes related to rainfall distribution pattern and tidal sea water incursion. Air temperature (25 35?C), water temperature (26 32.5?C), total dissolved total (656 19611.31 mg/L), dissolved oxygen (4.15 6.83 mg/L), transparency (22.5and 135cm), pH (6.73 7.59), salinity (23.24‰) and calcium (4.69258.17mg/L) recorded increased values in the dry than wet season. On the other hand biological oxygen demand (1 4mg/L), chemical oxygen demand (4 18mg/L), total suspended solids (1 38mg/L), nitrate (0.19 12.85mg/L),copper (0.0020.004mg/L), zinc (0.01 and 0.057) and cadmium (0.0006 0.0018mg/L) recorded higher values in the wet season. Chlorophyll a, chlorophyll b and pheophytinavalues were higher in the dry season. Notable correlation coefficient (r) was recorded between chlorophyll a and nitrate (r = 0.73, p< 0.05), phosphate (r = 0.82, p< 0.01), chemical oxygen demand (r = 0.35, p< 0.01), biochemical oxygen demand (r = 0.22, p<0.01)and copper (r = --.387, p<0.01). On another hand correlation between chlorophyll b and rainfall (r = 0.62, p< 0.01), pH (r = 0.31, p< 0.05), zinc (r = 0.44, p<0.05), manganese (r = 0.36, p< 0.05) and cadmium (r = 0.33, p< 0.05)were noteworthy.Furthermore phaeophytina showed a correlated relationship with rainfall (r = 0.39, p<0.01), dissolved oxygen (r = 0.31, p<0.05) and cadmium(r= 0.36, p<0.05). Recorded chlorophyll a values place the western Lagos Lagoon between the mesotrophic and eutrophic status. Increasing nitrate (nutrient) levels coupled with the reduced rainfall events led to the development of more algal cells (phytoplankton) thus higher algal pigments level within the western Lagos lagoon ecosystem.