The study was conducted to assess the spatial and seasonal variations of macroinvertebrates into two small marginal lagoons in the South-eastern of Côte d’Ivoire. Macroinvertebrates were obtained monthly using a hand net, a van veen grab and an artificial trap from September 2015 to August 2016. Physical and chemical parameters were quantified using standard methods of analysis. Analysis of the physical and chemical parameters in both lagoons showed significant seasonal variation, except for pH, nitrite and ammonium. We identified 145 and 105 macroinvertebrate species composed of aquatic Insects, Achaeta, Gastropoda, Crustacea and Arachnida respectively in Ono and Hébé lagoons. Megaloptera, Amphipoda and Basommatophora were only found in Ono lagoon whereas Lepidoptera was only present in Hébé lagoon. The highest values were found in dry season (127 taxa) and rainy season (126 taxa) in Ono lagoon whereas in Hébé lagoon, the highest values were found in dry season (93 taxa). The Shannon diversity index and evenness values of 3.72-4.25 and 0.84-0.91 respectively in both lagoons indicate that the macroinvertebrate stands are relatively diversified and balanced. However, the increase of anthropogenic disturbances on these lagoons constituted a real threat of the macroinvertebrates at long term.