Gaelle, It depends much more on rains/snow melting and local organic and chemical pollution. I think every river except ones in deserted areas can have unique profile with some general trends influenced by local climate and landscape.

http://www.ars.usda.gov/SP2UserFiles/Place/20360500/pdf_pubs/P2381.pdf http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0092579

http://link.springer.com/article/10.1007%2Fs10661-006-1508-4#page-1

http://www.tandfonline.com/doi/abs/10.1080/09593339309385322#.VD1S0Hu9rto

Thank you very much! This helped me a lot!

The general rule is that bacterial activity is correlated to water temperature and organic matter aka. Biological Oxygen Demand (BOD).  There are ways to discover this for whatever body of water you are looking at.  If you observe your oxygen curves, the period of time where the daily swing in dissolved oxygen is greatest will be your highest activity.  In some cases the period of time following a strong wind storm, during the growing season, can result in periods where the dissolved oxygen remains near zero.  This would likely be your highest bacterial activity.  Depending on your local flood conditions, BOD can be highest if the temperatures are high and there is significant organic debris on the floodplain.  In the Mississippi River Basin flooding usually occurs during the winter/early spring when temperatures are low, inhibiting bacterial action.  

If you are looking at high gradient streams with flashy hydroperiods, or low gradient streams with long flood durations makes a big difference, also floodplain interaction.

Every stream has it's own bacterial signature but temperatures near 0C result in very low activity and near 30 or higher results in very high activity assuming an adequate supply of food.

Thanks a lot for your answer! do you know any other parameter I could measure to assess biological activity? dissolved oxygen variation maybe?

There are a lot of indirect ways that have been used. Some people do actual cultures to determine concentrations of specific bacteria.  People have used 3H-leucine (Smith and Azam 1992, Marine Microbial Food Webs:6 pp 107-114. 

You can make assumptions from the diel oxygen cycle but that cycle is effected by algal production of oxygen. which is effected by many other factors, are you considering algae to be bacteria as well?

To determine the lowest bacterial and algal activity period you would find the time period when Oxygen concentrations are around or closest to 100% at night and during the day.  If no other factors like nutrient pollution are occurring this will be during the coldest water temperature times of year.

I want to rule out biodegradation regarding bacteria (and any other organism that degrades xenobiotics independently from sunlight). Algeas are tricky, it's biodegradation but photodependent one (as I guess they don't degrade micropollutants during the night). So I'm thinking of assessing xenobiotics elimination in rivers in winter (at a temperature close to 0) during night and day. I guess at these conditions, neither bacteria nor algeas are active(?).

not much happens around 0.