How do hydroelectric dams affect river systems?
I would argue they have a profound effect.
A river is a highly dynamic system, providing a huge range of habitats and food, transporting nutrients and minerals from the uplands to the sea.
A hydroelectric scheme on a river will generally (not always) involve a dam and the stopping of the natural flow (and variation in that flow) to generate power that fundamentally changes the nature of the river. The flow rate will then be carefully controlled to produce electricity when demand (hence profit) is highest and no longer have the constant variation (both annual and chaotic variation in amplitude) of a ‘natural’ river.
The dam will also cause nutrients and silt to settle out changing the distribution of both downstream and making it harder (or impossible) for spawning fish to climb higher in the river system to the habitat they require (often sand/gravel in my own limited experience.) Some power companies have attempted to mitigate this effect by providing “fish ladders” of varying design and success.
Finally, all HEP systems will introduce some pollution via grease/oil etc used in the turbines, valves and vanes used to direct the flow of water and extract energy from its flow.