Will my filtration / pumps kill the Copepods?

Copepods are very hardy marine organisms accustomed to the strong ocean currents found on natural coral reefs.

Typically the water movement in an aquarium is significantly less than in the ocean.
Copepods have no problem navigating your aquarium, finding rocks, macro-algae, and other hiding places where they can live and carry out their life-cycle in your aquarium.
They are also small enough to fit in between the blades of circulation pumps so they are not killed if and when they do pass through one.

We do suggest (In this help desk article) that you turn off your pumps for 30 minutes to an hour, and remove filter socks for up to 24 hours.
Once your pods have found places to hide they will multiply rapidly and help clean and feed your tank!