As others have said, the smell comes from the sea grass that washes ashore on the beach on Padre Island and in Flour Bluff simply due to the direction of the water currents. The smell comes from the plant material decaying and it does smell worse in the summer when the sun is baking it all day.
The water currents and weather determine when it washes up and how much there is. It varies based on these factors, but there is always going to be some certain times of the year due to the currents. The currents change in the fall and there is usually a lot less to none, unless there has been a storm.
Nearly all beaches deal with seaweed to some degree. When you live on the coast you find this out. When you visit a resort the machines were at the beach before you woke up scraping it all up for you!
I have lived in Flour Bluff for two years and just bought a lot in the bluff on the water and can tell you I have gotten used to the smell. As others have said, it doesn't smell all the time (or even most the time IMHO) and that also has to do with wind direction on any given day.
Regarding the mucky shoreline and getting in the water....The Laguna Madre is different than the ocean. The shore is a mix of sand and mud and decayed seaweed, so it will be mucky along the shore in most spots. Not that many people really "swim" in the Laguna Madre. If you go out in a kayak or a boat you can easily find what's called "pot holes" which are large open areas with a sandy bottom. I personally think those are great places to swim especially on those days when the water is crystal clear (also caused by the currents and wind). You can break out the snorkle mask and have a great time.
My wife and I moved to Padre Island 3 years ago. The smell your talking about in the area is the sea grass you see along the shore as your driving from Floue Bluff to the Island. The strength of the smell comes and goes, but it is the natural result of decay. To address the beach question. The weed, as it is called, comes in around March to May. How long it stays depends on a lot of factors, ie. water currents, water temps, number of storms in the Gulf, etc. Usually the weed clears in the fall when the water temps start to drop.
The weed is a mess on the beach and we always take a shovel and rake when we go to the beach. The city and county do a good job of scraping the weed and this process helps build a great foundation for the dunes. Also the weed, while it out to see is a great home for sea turtles, crabs and small marine creatures to live and escape fish. The best news is that as the weed comes into close shore a lot of big Red fish, Trout and Shark swim in the weed looking for dinner.
To sum up. If your going to live on the Island and enjoy the beachs take something for your sinus', a shovel, rake, and enjoy the fact that we live and share in a great enviroment for wild life. Other wise Destin Fl. would be the place to go if your wanting a pretty beach, snow white sand, and not much wildlife.
FYI: Big Reds are in the weed off the Packery Jetty now hitting on 3" live mullet. I saw a couple of nice size fins also. So take some Shark tackle and have some fun.
Call me if I can help you with your real estate needs. See you on the beach
If you move towards the intercoastal waterway (Padre Island) the smell seems to go away.
The smell does not happen every day of the year anyway.
Also depends where you want to live and how much you want to spend.
Any questions, I will be glad to help.