MTGNexus

I have the card Eyes of the Watcher on the battlefield.
I cast an instant say Brainstorm. Can I respond to my own Brainstorm on the stack by sacrificing Flooded Strand before I want to pay the 1 to scry 2? Is there a window of opportunity to respond to my own spell before I need to pay for the Eyes of the Watcher first?

Yeah, you're free to activate other abilities while a triggered ability is on the stack. Paying the cost in Eyes of the Watcher is part of the resolution of the triggered ability - you don't need to have 1 available till it resolves.