Once the duo has left the area, turn right and reach the end of the alley. You'll find an empty canister - take it with you. Double back and proceed forward to reach the bridge which will allow you to get through to the other side of the dock. You should notice a blue barrel right next to a propped ladder - perform a close-up to check its contents (hydrochloric acid), then use the tap to fill the canister with the liquid.
Turn around and make your way to the boat at the end of the alley - along the way, you can attempt to turn off the tap which spills contaminated liquid into the water, but Kate won't be able to do that on her own.
The boat is flimsy, but should survive a short journey. Equip the canister and pour the acid on the chain to unhitch the boat.