What factors can affect river species diversity?

Many factors influence the alpha diversity found in a riverine ecosystem including age of the river, dissolved oxygen, organic matter, total suspended solids, pollution, introduction of invasive species, dams and changes to the river flow all affect biodiversity.

Generally speaking, greater heterogeneity leads to more niches available for exploration and more species exploiting those niches. Hence, a stream that varies in width, depth, organic matter, available sunlight, and other biophysical characteristics is going to be more diverse that a stream that is consistent in those same factors.

More organic matter (dead leaves and such which act as a source of food) generally leads to increased diversity(see here).

Higher levels of total suspended solids in the water is linked to lower diversity (see here).

Daming rivers or changing their flow is typically harmful and leads to lower diversity, as does pollution and the introduction of invasive species.

Stressors affecting San Francisco Bay Delta water quality, habitat condition, and ecosystem structure and functioning:

You can read more about threats to river diversity here.