Benthic macro invertebrate communities were collected at six different sampling sites in the Musucheon stream in Korea from July 2006 to July 2007, and ecological exergy values were calculated based on five different functional feeding groups (collector-gatherer, collector-filterer, predator, scrapper, and shredder) of benthic macro invertebrates. Each sampling site was categorized to three stream types (perennial, intermittent and drought) based on the water flow condition. Exergy values were low at all study sites right after a heavy rain and relatively higher in the perennial stream type than in the intermittent or the drought stream type. Self-Organizing Map (SOM), unsupervised artificial neural network, was implemented to pattern spatial and temporal dynamics of ecological exergy of the study sites. SOM classified samples into four clusters. The classification reflected the effects of floods and droughts on benthic macroinvertebrate communities, and was mainly related with the stream types of the sampling sites. Exergy values of each functional feeding group also responded differently according to the different stream types. Finally, the results showed that exergy is an effective ecological indicator, and patterning changes of exergy using SOM is an effective way to evaluate target ecosystems.