Lake water quality systems are extremely complex and every lake is characterized by many complicated interactions between biological, chemical and physical variables. One of the most important tasks of lake mechanism analysis is to examine the relations among important water quality variables and to describe such complicated relationships quantitatively, simply and practically. Lake Biwa was chosen as a target lake, where a periodic water quality investigation was conducted every month from 1979 at 50 sampling sites. The objective of this study is to establish an application procedure of three-ways layout data and to present a vision including its practical result, expecting that this vision may also provide a direction for further research. The results showed that (1) cluster analysis following the three-ways layout ANOVA method is very effective in presenting water quality variation, (2) correlation analysis of water quality indices in each effect of parameters and their interaction between two items verifies that their relationships in parameters are different due to different mechanisms. (3) An integrated analysis procedure was derived, potentially describing those data in forms which convey their important characteristics and reveal their significant relationship. The same approach of this analysis procedure could be possibly applied for other water quality indices in other lakes.

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