Land use changes due to urbanization are going to affect your flows MUCH MUCH MUCH more than "climate change" will.
I know urbanization isn't the sexy thing to research, because Goldman Sachs isn't dumping all sorts of money into "parking lot cap and trade," but it's your primary culprit for the environmental issue you're researching.
When you're talking about an estuary, basin urbanization will have two important effects. 1) the event flood flows (during/after storms) will be much higher. 2) the base flows (between storms) will be much lower. If you're working on a paper, and you're trying to dig up some stuff related to Alabama watersheds, do some research on the Apalachicola River and Apalachicola Bay. It's estuary has been majorly effected by urbanization in Atlanta and along the Chattahoochee/Flint, doing quite a bit of damage to what was once the most productive oyster fishery in the country. Where the water used to always be brackish, now it's either too salty between storms or too fresh after storms, because of how urbanization interferes with they hydrologic cycle. I'm sure quite a bit has been written about it, since it's a central element of the Southeastern Water Wars.
The first thing I'd do if I were you, is contact FEMA and pull the HEC-RAS model for the river you're working in, and ask them if they have a "future condition" model. The work may have already been done, at last for the 100 year storm. I know many municipalities will maintain multiple flood models, one for now and one for "future land use," based on their zoning plans and growth projections. Don't know if such a thing exists on a large scale though.
If you ultimately wanted to put together a 2050 hydrologic model of the whole basin and compare it to the current one, then that's a task of Masters Thesis complexity. You would need to create a hydrologic model of the entire basin based on 2050 land use mapping, and do some hydraulic analysis of it. The two obvious software packages to use would be HEC-HMS and HEC-RAS, but you might be able to do the whole thing in EPA-SWMM. Those being the free options, there's also plenty of $$ software that could do it.
Hydrology, Drainage Analysis, Flood Studies, and Complex Stormwater Litigation for Atlanta and the South East -