Modelling fish co-occurrence patterns in a small spring-fed river using a machine learning approach

•Random Forests multi-class classifier analyzes co-occurrence patterns of four fish species.•Multi-class habitat suitability model can assess habitat conditions of species co-occurrence.•Class prevalence matters in multi-species habitat suitability modelling.•Variable importance and partial dependence plots extract ecological knowledge.•Multi-species model is useful for wildlife conservation and control against alien species.