Mystic Seaport Pond is a very small (0.3-acre) pond located near Mystic Seaport. It was surveyed in August 2006. This pond is notable for its very large population of hydrilla (Hydrilla verticillata), a highly invasive plant that is very rare to Connecticut. This plant is found everywhere in the pond, except for the deeper basin to the north.

Other submerged species that were found included marsh primrose-willow (Ludwigia palustris) on the eastern and south western shores, broadleaf arrowhead (Sagittaria latifolia) lining the shore on the southern 1/3 of the pond, and floating-leaf pondweed (Potamogeton natans) in very small patches in the middle of the western shore and in the southeast corner. Emergent species include cattail (Typha species), found along the perimeter on the northern shore, southwest shore, and in a large patch in the middle of the western shore. Pickerelweed (Pontederia cordata) is also found in these places, as well as on the southeast shore. The floating water lilies, white water lily (Nymphaea odorata) and yellow water lily (Nuphar variegata), are mainly clustered on the north and south shorelines.