You can anchor there...
...but with caution. There are a number of reefs in that harbor, but if you are careful then you should be OK.An alternative is to go up into Mystic. I understand from a Mystic handout that there are 7 town moorings up thru the second bridge and just beyond Mystic Seaport off the side of the channel.Then you can tuck in behind Mason Island if you are in a pinch. But be very careful and check your charts. There is a reef there that many people hit because they misread their charts.Of course there are also many marinas along the Mystic River. I stayed at Noank Village Boatyard on a mooring for $25 this summer. And very nice amenities, free launch service and nice people there.