Demographic pressure on watercourses in Côte d’Ivoire is causing increasing degradation of water quality. One of the indicators of water quality is the micro-algal population. The aim of this study is to assess the trophic status of the waters of the Comoé River, based on physico-chemical parameters and micro-algal populations. Four sampling campaigns were carried out from February 2020 to January 2021 at ten selected stations on the river. Abiotic variables were measured in situ and in the laboratory. Microalgae were collected using a plankton net and observed under photonic and electron microscopes for identification. Several indices for assessing the trophic status of the waters were calculated. The study revealed that the waters are relatively warm, rich in nutritive salts and not very transparent. A total of 190 taxa in 79 genera, 39 families, 23 orders, 10 classes and 5 phyla were identified. The Euglenophyceae class, with 58 taxa (30.52%), is the most diverse. The calculated A and B indices range from 6.14 to 7.69 and from 1.14 to 2.23 respectively. The C index fluctuates between 0.20 and 1.18. Nutrient concentration, transparency values and the A, B and C indices indicate that the river’s waters are eutrophic, with more pronounced eutrophy in the middle and lower reaches.