There's been many times when Gertrude the Fish died. In the Pilot episode where Nell vacuumed the fish by accident, when Nell fed her Comet rather than fish food, and one time when Nell gave them water that wound-up contaminated.

Gertrude to me was Kenny before Kenny was getting killed!

Was there any other times when Gertrude died?

she died during that ep when sam freaked out during an earthquake