"To win silver is a great achievement. It felt rough out there and it was hard and it did not come together how we would have liked it to," she said.
"Our qualification round this morning was great and we did a time we were really happy with. We have two more events coming up, both on the road and we are now going to focus on these and continue to give it our all."
Thompson won a Gold, Silver and Bronze and broke a World Record at the London 2012 Paralympic Games with her former stoker, Phillipa Gray (now retired). The British tandem of Turnham and Hall were simply too fast, taking the win by over 3sec in 3:28.050.
The pair will now look to the road for a chance at a medal in the 30km road trial.
Meanwhile, Sophie Pascoe has broken her own world record on route to another gold medal.
Racing in the SM10 200m individual medley, Pascoe shaved half a second of her previous record with a time of 2:24:90.
She got a bit of revenge on Canadian Aurelie Rivard, who beat her in the 50m freestyle final.
Northlander Cameron Leslie will be in the pool tomorrow, racing in his favoured SM4 150m individual medley. Leslie is the current world record holder and two-time defending Paralympic gold medalist in the event.
The heat is at 1am and the final, should he make it, is at 8:50am.