How to do hierarchical cluster analysis for multivariate data sets with multiple data for each sets?

Hello, I am trying to do hierarchical clustering analysis of water quality data . I have 11 data sets with seventeen parameters arranged in columns with more than 100 observations for each parameters. The confusion I am having is of not knowing if I use all the data for each station in clustering or use the maximum value obtained after Z-scale transformation. If I have to use all the data I do not know how to associate data with appropriate site. For example data set for one site is 100*17 and in total it would be 1100*17. But after arranging data in the manner of 1100*17 if I carry out the clustering it will give me 1100 clusters. Even if I limit the number of clusters at 11 I do not know whether the appropriate data points fall in the appropriate cluster. Thanks