In order to assess ecological status for all Community waters (UE Water Framework Directive), France use the standardized global biological index (NF T 90-350) and the diatom biological index (NF T 90-354).
IBGN assesses the biogenic tendency of a waterstream station from the results of a macrofauna analysis that is considered to produce a comprehensive expression of the general quality of a waterstream station under otherwise constant conditions. When applied to an isolated site, the method determines the global biological quality within a range of parameters, whose maximum value corresponds to the optimal combination of set variety with the nature of the benthic macrofauna. When applied comparatively (e.g., upstream and downstream from a discharge), the method evaluates the effect of a disturbance on the receiving environment within the limits of its sensitivity.
The benthic macrofauna samples (diameter > 500 µm) are taken at each station, according to a sampling protocol that takes into account the different types of flexible net (diameter = 500 mm), using: retractable panels, removable base (1/20 m2), sampler "Surber" position, rack, metal frame, cutting blade, sampler "Shrimpnet" position, and habitats defined by the support structure and the flow speed.
For Macro fauna you have to do direct identification and for zoo-plankton direct identification with the help of online identification guide and "Practical guide to identifying freshwater Crustacean Zooplankton"
Dr K, Kick sampling is a standard method that is used in shallow rivers and streams and then make the counts. The fastest method is to use the Abundance and Distribution range and this involves several samples (Distribution) and the abundance score of low, medium and high are to be decided by the field worker for a specific area (a stream section) and a specific time (perhaps when water levels are low). This is part of the biopollution method which can be obtained from:
Olenin S, Minchin D, Daunys D (2007) Assessment of biopollution in aquatic ecosystems. Marine Pollution Bulletin 55(7-9): 379-394
This is a very fast method and it means that you can cover most sites.
So much depends on the precise levels you require for your specific purpose.
Here are my 2 online publications that should be of help for sampling stream and riparian macroinvertebrates and meiofaunae:
Vadas, R.L. Jr. 1997. Assemblage structure of riparian and drifting invertebrates along environmental gradients in two streams of southern British Columbia. DOE FRAP (Canada Department of the Environment, Fraser River Action Plan) 98(28): 62 pp. (http://research.rem.sfu.ca/frap/9828.pdf).
Vadas, R.L. Jr. 1998. Human impact on aquatic and riparian ecosystems in two streams of the Thompson River drainage, British Columbia. Pages 13-30 in M.K. Brewin and D.M.A. Monita (eds.). Forest-fish conference: land management practices
It is very important what organisms are you interested in! The overall estimation of the stream health may be depicted using all organisms but in order to have secure and precise estimation of the water quality algae are most certainly the best possible choice. Here is one opinion that might not be approved by many scientists, but it may help you decide what to do! Best regards
The attached might be useful. It's very much slanted towards species conservation rather than use of the invertebrates as proxy indicators of stress, but the upside is that it's nice & short! It's a review draft, so ignore the odd mistake.