The main obstacles to monitoring aquatic ecosystems have always been the lack of data, the complex socio-economic context and the lack of specialised expertise that characterise the West African region. To overcome these challenges, it is necessary to invest in the definition of context-appropriate approaches that allow good ecological assessment, improve understanding of the functioning of these ecosystems and facilitate data collection. This study focused on using benthic macrofauna to assess the risks of moving away from Good Ecological Status towards the functioning of an anthropised system (Nokoué-Benin), based on the definition of reference values for macroinvertebrate metrics, stress thresholds and the responses of selected metrics to stressors. The approach used is a combination of a joint species distribution model and Bayesian networks. We used JSDM to select relevant metrics and generate posterior probabilities. We then converted these posterior probabilities into posterior response probabilities for each of the stress levels and fed them into a Bayesian network. We used the Bayesian network response predictions to define the reference values of the metrics and the stress thresholds derived from the probability density plots for the low pressure levels. An application of this approach was then carried out on a lagoon sampled during high and low water periods for three years, with 33 macroinvertebrate taxa present in all seasons and sampling points, and measurements of 14 environmental parameters used as application data. The relevance of the results, despite the small sample size, supports wider application of the approach in West Africa.