Putting in at Back Creek Park in Yorktown gives you a chance to take one 3-hour trip that feels like two different outings.
When you put in at the boat ramp and turn left you paddle by many nice homes and old fish processing plants. There is also an abundance of Osprey nests with fussy inhabitants. As you get to the mouth of the creek there is Seaford Scallop, a large Scallop processing plant with many large fishing boats.
Here is where you notice a change from a quiet lazy paddle through a relatively quiet narrow creek to a much larger body of water. You probably need to take care here as there are many commercial fishing boats of all sizes coming and going in the channel. Stick to the shallow water to insure you stay out of their way. At the mouth of the creek make a dash across the channel - to your left will be the "Thoroughfare" that takes you out to the York River.
Once across the channel you will be near the Goodwin Islands. Again the atmosphere changes back to a much quieter still water paddle. As you get closer to the islands you can start to explore. Much to my disappointment the island is off limits as it is a wild life refuge but it is still very exciting to paddle around. We made our way along the banks of the island and found a very small path THROUGH the islands and out to the York River. As you paddle along here make sure you explore every nook. We almost gave up on a couple of paths only to find that they went much further into the island than first appeared.
After coming out into the river you feel like you are paddling on big water again. The York River is very wide at this point and light breeze can kick up quite a chop. Making your way back around the island and up the Thoroughfare requires you to watch out for more boat traffic. Again stay in the shallows until you have a break to cross the channel.
Nice boat ramps with floating docks. Also tennis courts.
Take Route 17 North into Yorktown. Turn Right onto Goodwin Neck Road. Go down through 2 stop lights, past the oil refinery and Back Creek Park will be on your right.
A map that shows good detail of the Goodwin Islands would definitely help you explore.