The ecosystem health of rivers downstream of dams is among the issues that has become focus of attention of many researchers particularly in the recent years. This paper aims to deal with the question, how the environmental health of a river ecosystem can be addressed in water resources planning and management studies. In this study, different parameters affecting the ecosystem of river-reservoir systems, as well as various biological components of river ecosystems have been studied and among them, benthic macro-invertebrates have been selected. Among various bio-indices, biodiversity indices have been selected as the evaluation tool. The case study of this research is Aboulabbas River in Khuzestan province in Iran. The relationship between the biodiversity indices and physicochemical parameters have been studied using correlation analysis, Principal Component Analysis (PCA), and Genetic Programming (GP). Margalef index was selected as the appropriate bio-index for the studied catchment area. The relationship found in this study for the first time between the Margalef bio-index and physicochemical parameters of water in the Aboulabbas River has proved to be a useful tool for water resources managers to assess the ecosystem status when only physicochemical properties of water are known.