It all depends
on what you like most -- destination cruising or shortest distance to your boat.I have been on the upper bay now for nine years. I have berthed Explorer at Owens, Perryville Yacht Club, and Tidewater. Havre de Grace is a charming small town, with many good restaurants and shops. There are several marinas to choose from, but Tidewater is unquestionably the nicest one, and the most expensive.On the other side of the river (technically, I believe the Susquehanna River ends and the Chesapeake Bay begins at Havre de Grace), Perryville has two marinas, but you need to get under the Amtrak bridge to get there (the charts show this as a swing bridge, but the local word is that you have to pay Amtrak to open it -- otherwise, your mast needs to be less than 50'). Owens has a pool, but most of its slips do not have shore power. Owens is also very shallow in places, and even in my next-to-the end slip, I can get hung up at low tide. A little farther north is Port Deposit, which appears to have one marina, although I have heard it is part of a condo complex. The town is very quaint and at least worth a visit.As the many other posters here have pointed out, there is a trade-off between more driving time if you keep your boat lower in the bay, versus less driving time for the upper bay. The link I've inserted is to the website for a local sailing school which gives cruising destinations and travel time from Havre de Grace. I-95 can get very congested around the Delaware tolls and the Churchman's area where SR1 (shore traffic) merges. But, there are many alternate routes. US1 is the easiest way to travel from the MD border to Kennett Square/West Chester, not I-95. Even if you decide to use I-95, at least cross the Susquehanna on US40 using the Thomas J. Hatem Memorial Bridge. The toll on this bridge is the same as on I-95, but you can buy an annual bridge sticker for the cost of a single toll ($5). The sticker is only valid on the Hatem bridge.As for water quality, I was unaware there was a problem with "toxic algae". If this is the thick green "pea soup" you see in places, I don't see how it would affect sailing or swimming, as the pea soup usually congeals in shallows or stagnant areas. I have always felt the water is better in the upper bay for swimming, especially when I hear stories about sea nettles and jellyfish in the more brackish middle bay. Half the time I go out on my boat, I end up anchoring out on the flats (the large, shallow expanse abeam Havre de Grace) and just chilling out. It's a great place to swim. I have sailed to Baltimore many times, but my favorite "destination" is Georgetown on the scenic Sassafras River.