The water quality characteristics and phytoplankton at a domestic waste polluted site at Oworonsoki, Lagos Lagoon in relation to environmental factors were investigated for six months (October, 2012 – March, 2013). Plankton samples were collected horizontally with plankton hauls on each trip using standard plankton net of 55µm mesh size tied unto a motorized boat and towed slowly  (≤4m/s) for 10 mins. The water quality characteristics showed monthly variation linked to hydrological flow conditions, namely the rainfall pattern and tidal seawater inflow. Air temperature (28.3 – 32˚C), Water temperature (29 - 31˚C), Transparency (12.95 – 101.5cm), Total suspended solid (8 – 35mg/L), Total dissolved solid (553.0 – 20712.66mg/L), Conductivity (1069.0 – 31100.0µS/cm), Salinity (0.50 – 17.11 %), Acidity (4.9 – 6.3mg/L), Total hardness (102.0 – 3811.0 mg/L), Dissolved oxygen (4.8 – 5.2 mg/L), Chemical oxygen demand (14 – 23 mg/L) recorded higher values in the dry than in the wet season. High nutrients, especially nitrates and heavy metal levels between December and February points to the inflow of domestic wastes. The water quality characteristics reflected freshwaters situation in October and November (0.52 – 0.82 ‰) while December through March were increasingly brackish (9.42 – 17.11 %). The phytoplankton diversity (S) and abundance (N) were notably higher in the dry than the wet season. The phytoplankton spectrum (Bacillariophyta, Cyanophyta and Chlorophyta) were dominated by the Bacillariophyta (Diatoms) (93.47% - Centrales – 69.77 % and Pennales – 30.23%).  Notable species of  were Aulacoseira granulata var. angustissima, Odontella laevis, Coscinodiscus radiatus, Skeletonema coastasum, Chaetoceros convolutes, Bacillaria paxillifer, Gyrosigma balticum, Nitzschia sigmoidea, Synedra crystallina, Thalasiothrix fraunfeldii, Synedra ulna, Microcystis aeruginosa and Oscillatoria limnosa. The phytoplankton diversity at each time was reflective of the water chemistry situation. Comparatively, low phytoplankton diversity, and the occurrence of indicators of organic waste pollution are noteworthy.