Applied Environmental Data Analyses: Water Chemistry and Biota

I left academia and basic ecological research decades ago and now work
with environmental data collected by companies in compliance with regulatory
permit requirements. I've bought and read (mostly) all the books I could
find on ecological analyses using R (all but one of Alain Zuur's books,
Legendre & Legendre's 2nd English edition, Mike McCarthy's Bayesian methods
book, and Ben Bolker's book) but cannot find any references to 'communities'
in the indices. I'd greatly appreciate pointers to sources appropriate for
environmental data (which is much sloppier than ecological research data).

   The last time I addressed community analyses was my post-doc research
which I published in Freshwater Biology in 1984. Only within the past year
have my clients needed to address issues using benthic macroinvertebrate
assemblages (and fish) in streams. And, since I work by myself, I've no one
with whom to share ideas and discuss approaches; perhaps there's a better
forum than this mail list for this.

   The available benthic data has little taxonomic consistency below the
family level. I want to use functional feeding groups rather than taxa as
the basis of comparison because those better reflect conditions in each
stream (collections of biota are made only once per year), and I want to
examine correlations and cause-and-effect relations between biotic
assemblages and water chemistry. There are only a few fish collections,
tool, in the available data.

   All ideas are certainly welcome!

TIA,

Rich