A counterpropagation neural network (CPN) was applied to predict species richness (SR) and Shannon diversity index (SH) of benthic macroinvertebrate communities using 34 environmental variables. The data were collected at 664 sites at 23 different water types such as springs, streams, rivers, canals, ditches, lakes, and pools in The Netherlands. By training the CPN, the sampling sites were classified into five groups and the classification was mainly related to pollution status and habitat type of the sampling sites. By visualizing environmental variables and diversity indices on the map of the trained model, the relationships between variables were evaluated. The trained CPN serves as a 'look-up table' for finding the corresponding values between environmental variables and community indices. The output of the model fitted SH and SR well showing a high accuracy of the prediction (r>0.90 and 0.67 for learning and testing process, respectively) for both SH and SR. Finally, the results of this study, which uses the capability of the CPN for patterning and predicting ecological data, suggest that the CPN can be effectively used as a tool for assessing ecological status and predicting water quality of target ecosystems.