Replicating a large-scale habitat to a miniaturized is not very easy. In order to make it possible, here are some points.
1. Try to narrow down your research to what are you looking for in the Hudson River. It may be 'polluted' as reported, but you have to actually determine what are those pollutants and what do you want to know. For example you are looking for the effects of cadmium ions present in water systems that can cause detrimental disease in human. You can't just put all the things you've researched in the net about the content of the river. Say, you are going to add amounts of heavy metals, furans, dioxin and PAH's. That's not going to work since you have to but those chemicals and get a very small amount.
2. Next you do not need to show a moving water to show a river but a motor can do. Get the motor similar to that with the aquarium and attach it to the water systems.
3. In setting up your miniature river, it would be better if you will create two ecosystems: one with polluted water and the other one with clean water. Put some plants and animals (worms, insects and anything you found in your garden) in both set-up and see if there is a difference in their growth and metabolism.
4. be sure that your ecosystem is secured and enclosed. You can do that in an aquarium so that plants can have access to sunlight even if it is tightly secured.
Pollutants in the river can be transferred in the soil and atmosphere and eventually to the living systems that can affect their growth and existence.