They have been able to excavate the fort, because of the decaying wood. There was a triangular fort, with turrets for canon in each corner. They arrived in a period of drought, and the river would have been down, and backed up. Consequently the men would have been drinking salt water, which likely cause salt poisoning. It wasn't until there was a good rain that conditions improved.
John Smith returned to England for medical attention. His powder bag exploded. It likely was the cause of a murder attempt, although could also have been accidental. At any rate, he returned to England, which likely saved his life, as most of those in Jamestown had a short life expectancy. It is likely famine continued to take its toll. The settlers ate anything they could, their pets, their horses, and even perhaps exhuming graves to eat the bodies. The dying season, as it was called, about 1610, was caused by the bubonic plague, likely brought by a resupply ship. During this time, bodies were buried quickly, often two to a grave. They were buried inside the fort.
The colony very nearly failed. They came looking for gold, which they did not find. It wasn't until they found a stable crop--tobacco, that they began to prosper.