The phytoplankton community using microscopy and algal pigment concentrations at the western and eastern parts of the Lagos lagoon were monitored from November, 2015 to April, 2016 in relation to water chemistry changes. The phytoplankton spectrum and water quality parameters showed monthly variations linked with flood water inflow connected to the rainfall distributive pattern and tidal water incursion into the lagoon. Whereas salinity, total dissolved solids, conductivity, acidity, dissolved oxygen, total hardness and sulphate generally increased from November to April during the study period, total suspended solids, silica, pH and biological oxygen demand reduced likewise for both parts of the Lagos lagoon. Microscopy revealed a total of 17 phytoplankton species that consisted of three (3) major divisions. Diatoms (93.88%), blue-green algae (5.91%) and green algae (0.21%). Notable species were Aulacoseira granulata var. angustissma, Coscinodiscus radiatus, Thalassionema nitzschioides and Oscillatoria sancta. The occurrence of Aulacoseira granulata var. angustissma and Oscillatoria sancta clearly defined the low salinity period (wet season effect) in November within the lagoon at both the western and eastern portions. On the other hand the occurrence of Coscinodiscus radiatus, Thalassionema longissima and Thalassionema nitzschioides recorded in brackish water conditions reflected a  period of increased salinity (dry season effect). Chlorophyll a estimates  ranged between 8 and 19 µg/L, chlorophyll b was from 0.5 to 2.8 µg/L and phaeophytin a levels were between 0.1 and 0.4 µg/L. For the western part of the Lagos lagoon, chlorophyll a was positively correlated with chlorophyll b and phaeophytin a, whereas for the eastern part, phaeophytin a was positively correlated with chlorophyll a but negatively correlated with chlorophyll b. Present species diversity and number of individuals (as determined by microscopy) show an obvious reduction in these parameters compared to previous studies. The negative correlation effects of heavy metals especially in the western axis of the lagoon are possibly limiting primary productivity in the phytoplankton crop. Nutrients are probably not readily bioavailable for commensurate photosynthetic processes.