In comparison with northern countries, limited data are available on the occurrence and potential toxicity of cyanobacterial blooms in lakes and ponds in sub-Saharan countries. With the aim of enhancing our knowledge on cyanobacteria and their toxins in Africa, we performed a 17-month monitoring of a freshwater ecosystem, Lagoon Aghien (Ivory Coast), which is used for multiple practices by riverine populations and for drinking water production in Abidjan city. The richness and diversity of the cyanobacterial community were high and displayed few variations during the entire survey. The monthly average abundances ranged from 4.1 × 10 4 to 1.8 × 10 5 cell mL −1 , with higher abundances recorded during the dry seasons. Among the five cyanotoxin families analyzed (anatoxin-a, cylindrospermopsin, homoanatoxin, microcystins, saxitoxin), only microcystins (MC) were detected with concentrations ranging from 0 to 0.364 μg L −1 in phytoplankton cells, from 32 to 1092 μg fresh weight (FW) kg −1 in fish intestines, and from 33 to 383 μg FW kg −1 in fish livers. Even if the MC concentrations in water and fish are low, usually below the thresholds defined in WHO guidelines, these data raise the issue of the relevance of these WHO guidelines for sub-Saharan Africa, where local populations are exposed throughout the year to these toxins in multiple ways.