Dear John, thanks a lot ... this is exactly what I searched for, best regards from Germany, Petra

which substances are you interested in? there is an incredibly large number of papers published - some general references but also some really interesting case studies are 

Buss, S., Cai, Z., Cardenas, B., Fleckenstein, J., Hannah, D., Heppell, K., … Wood, P. (2009). The Hyporheic Handbook - A handbook on the groundwater–surface water interface and hyporheic zone for environment managers (p. 264). Bristol.

Krause, S., Boano, F., Cuthbert, M. O., Fleckenstein, J. H., & Lewandowski, J. (2014). Understanding process dynamics at aquifer-surface water interfaces: An introduction to the special section on new modeling approaches and novel experimental technologies. Water Resources Research, 50. doi:10.1002/2013WR014755

Osenbrück, K., Wöhling, T., Lemke, D., Rohrbach, N., Schwientek, M., Leven, C., … Cirpka, O. a. (2013). Assessing hyporheic exchange and associated travel times by hydraulic, chemical, and isotopic monitoring at the Steinlach Test Site, Germany. Environmental Earth Sciences, 69(2), 359–372. doi:10.1007/s12665-012-2155-4

Tonina, D., & Buffington, J. M. (2011). Effects of stream discharge, alluvial depth and bar amplitude on hyporheic flow in pool-riffle channels. Water Resources Research, 47(8), 1–13. doi:10.1029/2010WR009140

Trauth, N., Schmidt, C., Maier, U., Vieweg, M., & Fleckenstein, J. H. (2013). Coupled 3-D stream flow and hyporheic flow model under varying stream and ambient groundwater flow conditions in a pool-riffle system. Water Resources Research, 49(9), 5834–5850. doi:10.1002/wrcr.20442

An ecological case study can be found in 

Schmidt, S. I., Hahn, H. J., Hatton, T. J., & Humphreys, W. F. (2007). Do faunal assemblages reflect the exchange intensity in groundwater zones? Hydrobiologia, 583(1), 1–19. doi:10.1007/s10750-006-0405-8 and

Schmidt, S. I., Hellweg, J., Hahn, H. J., Hatton, T. J., & Humphreys, W. F. (2007). Does groundwater influence the sediment fauna beneath a small, sandy stream? Limnologica, 37(2), 208–225. doi:10.1016/j.limno.2006.12.002

You could see the 'Hyporheic Handbook'. We published an extensive, downloadable, multi-authored volume called the 'Hyporheic Handbook' in 2009, which will have a great many references in its several chapters to your area of interest, Petra. The project was led by David Lerner.

The full Reference details are:

Buss, S. et al (2009). The Hyporheic Handbook - A Handbook on the Groundwater–Surface Water Interface and Hyporheic Zone for Environmental Managers (264pp.). Bristol, UK, Environment Agency, 280pp. (Science Report, SC0500).

It can be downloaded at:

http://nora.nerc.ac.uk/8643/

Google Scholar searches will add the more recent references. Hope that helps! Damian Lawler

Thanks ! ... regarding the question: the substances shall be pharmaceuticals.

ah, ok., pharmaceuticals is definitely something that I have NOT looked into .. so you may want to disregard all my suggestions ... 

We recently published a review article on hyporheic zone processes that might be of general value:

Boano, F., Harvey, J.W., Marion, A., Packman, A.I., Revelli, R., Ridolfi., L., Wörman, A., 2014. “Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications”, Reviews of Geophysics. doi: 10.1002/ 2012RG000417

It contains references to studies on mixing mechanisms and biogeochemical processes. 

We recently published a paper specifically on pharmaceutical transport in streams and for which the hyporheic zone plays a role for the substance transformation:

Riml. J. Wörman, A., Kunkel, U., Radke, M., 2013. "Evaluating the fate of six common pharmaceuticals using a reactive transport model: insights from a stream tracer test”, Science of the Total Environment 458-460 (2013) 344–354

Both articles can be downloaded via Research Gate.

Best, Anders 

Thanks !