The coronavirus (COVID-19) pandemic is the defining health crisis of our time. It has led to lockdowns of major cities and curbed industrial, commercial and vehicular activities. Lagos is the commercial and industrial hub of Nigeria and has the Lagos lagoon as the sink for the flow of wastes streams from all these activities.  Here we examine the water chemistry features and photosynthetic pigment parameters before the lockdown, during the lockdown and around the ease of the lockdown. Results show that parameters such as Dissolved Oxygen, Chlorophyll a and b, pH, Total Suspended Solids, Zinc, Copper, Lead, Chromium and Manganese increased considerably during the lockdown. On the other hand, parameters such as Conductivity, Total Dissolved Solids, Salinity, Acidity, Alkalinity, Total Hardness, Chloride, Sulphate, Phosphate, Calcium, Magnesium, Dissolved Inorganic Phosphate, Sodium and Chlorophyll c values reduced in the same period. In all, trends signify cleaner and clearer waters of the Lagos lagoon and these positive effects lingered during the ease of the lockdown period characterized by the cessation of major industrial and vehicular activities. During the lockdown, there were improved water quality conditions as well as primary production. The effects of seasonal variation in water chemistry factors including salinity were also noted.