Similar to prokaryotes, the variable regions of SSU rRNA can be targeted and used for high throughput amplicon sequencing.  A nice review of this approach specifically for protists is in the current issue of Journal of Eukaryotic Microbiology:  Hu et al. 2015. Estimating Protistan Diversity Using High-Throughput Sequencing doi:10.1111/jeu.12217  

http://onlinelibrary.wiley.com/doi/10.1111/jeu.12217/abstract

Hi. I know some tools for seek pathogenic protozoan, but should work for all protozoan. You can filter the river's water in celulosis-ester mebrane, and before proceed DNA extract. For PCR, conventional or nested, you can use general primers, For example Aplicomplex like genus Toxoplasma e Criptosporidium.

I don't do this myself but some of the labs that I work with will just use a Ion Torrent or MiSeq to basically get an idea of everything in a sample for a relatively low cost these days.  The biggest headache will be the algorithms and computing power to deal with terabits of sequence data.