There are many good ...

There are many good suggestions below , but I'll echo the sentiment that much more information is needed regarding your particular circumstance and add a word of caution against adopting another entity's design criteria without a solid understanding of the basis for those criteria and how they are similar or different from your project. What are the pollutants of interest and what are the flows? Do you need to reduce loads or minimize concentrations? Can you get by treating base flows, or must you capture and treat higher flows in order to meet the goals? I would recommend the book Treatment Wetlands, Second Edition by Kadlec and Wallace as a good starting point for general design information.  

As others have noted, the most effective approach may be to treat point sources, and non-point sources (tributaries) to the extent possible prior to those flows discharging to the main river channel. Once these inputs reach the river, the combined effects of dilution and increased flow, make it that much more challenging to deal with.