The only place I saw eel grass was in the deeper troughs of the Susquehanna Flats - not the rivers and creeks. And, I saw very little eel grass in the troughs - just small patches, which is better than no grass at all.
The dominant grasses were Eurasian Milfoil and hydrilla, both of which are invasives that were introduced by the aquarium industry. The most promising thing I saw, first hand, was a huge resurgence of freshwater clams on the Susquehanna Flats, which did an incredible job of filtering the water there. The clams ranged from 1 to 3-inches in diameter and a single scoop with a child's beach bucket produced 50 to 75 clams from the muddy, pockmarked bottom. Neat!
As for the water quality of the upper bay, particularly where I see hundreds of boats anchored each weekend all summer long, well, you be the judge. Most of the swimming activity takes place at Fishing Battery Island or the Spoils Island directly west of the Battery. Both islands have wide, expansive beaches, and Battery Island has been designated as a seabird sanctuary, thus prompting FWS to plant specific grasses on the island to attract seabirds. Consequently, thousands of gulls can be see sitting on the shores of the south beach daily and their droppings are more than 2 inches thick after just three years. Additionally, large numbers of cormorants can be found standing on partly submerged logs, rocks, and buoys (everyone knows what cormorants do.). Late afternoons is when a dozen or more American eagles arrive at the island, swooping down on migrating shad and herring, striped bass and sick and dying channel catfish that can be seen struggling on the surface. DNR has never provided me with a good explanation of why the catfish are dying in this are in relatively large numbers. DNR probably doesn't care because they have very little commercial value, and over the decades, DNR has shown that it is more concerned about commercially viable species.
Here's the really sad part. Unknowing boaters and their very young children are swimming in an area that is the confluence of several wastewater treatment plants. Just 4 miles up the bay is the Havre de Grace Basin, where the town discharges it's treated wastewater. Just across the mouth of the Susquehanna is Perryville, and the Perry Point VA Hospital, both of which have their own treatment plants and discharge their treated wastewater into the basin as well. Upriver, just four more miles is Port Deposit, which has it's own wastewater treatment plant, which is discharged directly into the Susquehanna River. A few miles to the east is Charlestown and it's antiquated wastewater treatment plant, which discharges into the middle reaches of the North East River. Across from Charlestown is the town of North East, which discharges it's treated sewage into the North East River's upper reaches. Just a short distance southwest of Battery Island is where Aberdeen Proving Grounds is situated, however, I believe their treated wastewater is discharged into Bush River, which probably would not reach the Battery Island area during an incoming tide. Don't know for sure, though. A small, treatment plant can be found at Swan Harbor, which is situated just northwest of the islands. As you can readily see, those folks, unknowingly, are swimming and bathing at the confluence of 5 sewage treatment plants.
Personally, when I take my children and grandson out on my boat and they want to jump in the water, I make them wait till I get back to the marina where they use the swimming pool. Not much of a chance of them contracting Mycobacterium Marinum in a swimming pool that is well maintained, but the odds have been increasingly greater in Chesapeake Bay over the past three decades, this despite claims the bay is getting cleaner. I, personally, only witnessed a single case of this insidious disease while working in the medical field. It was on the hands of a commercial waterman who scratched his finger on a crab pot while crabbing in the bay's upper reaches. He ended up having his finger amputated after nearly 6 months of intense treatment.
When the kids want to cool down on my boat, I have a solar shower that I suspend from a halyard, which does a great job. The shower is filled with tapwater at the marina before I leave the dock, it holds 5 gallons and does a great job. If it runs out of water, I refill it from my boat's water supply tank.
Now, after reading all this, plus the attached reports from Anne Arrundel County Health Department, if you still think it's safe to jump into the bay's waters, feel free to do so. The decision is totally up to you. Keep in mind, however, that there are people on this site that claim they have been jumping in the bay for decades and never got sick. But, when you do get sick from mycobacterial infections, you really get sick.
Good luck,
Gary