A comparative study of aquatic vegetation of 149 irrigation ponds in the surrounding area of Lake Shinji, Shimane Prefecture, Japan, was done to document the present status of aquatic flora and water chemistry. In addition, influence of 17 environmental factors on the between-pond variation in aquatic macrophyte composition was assessed by using detrended correspondence analysis (DCA). A total of 38 taxa were recorded, and the most frequent taxon was Trapa spp. (> 50~o). Number of taxa per pond ranged from 1 to 14 and mean number was 4.1. Floristic composition was primarily related to variation of the factors such as conductivity, Mg, Ca, Na, alkalinity, altitude, pH and depth. In contrast, no significant correlations were found with total P, PO4-P, transparency, COD, ignition loss of bottom soil, Mn and Fe. Of the 33 significant species associations between 19 species with more than 5Yo frequency occurrence, 28 were positive and the remaining 5 were negative. All of these negative associations involved Trapa spp., and not only water chemistry but some other factors like competition and bottom soil preference were assumed to influence species associations.