I can imagine a few solutions to the sea pollusion problem.
Have rain transfer pollusion from a water source to the ground within a certain radius. (I think it does this now? Or maybe it's the other way around... But it needs to be increased if that's the case)
Reduce the population growth for larger animals and introduce a way to catch larger amounts of fish, this way polutting the water will kill the migority of mid game protein. In the real world, we can only support our massive diets of livestock due to the industrialization of meat processing and organized animal farming. Outside of that, fish naturally appear in large numbers unless over fished by massive drag nets. Could even just nerf natural animal population growth and introduce a way to manage livestock (To secure a meat supply at a cost of a ton of farmed plants)
As for the bridge problem, I feel like that might end up with a rework of how building works. I don't like it personally but I think by adding cargo ships and giving them massive stockpiles, then large bridges will be seen as a huge waste of resources and inefficient by comparison.