Why did all of our goldfish die after we cleaned out the pond?

every spring my dad cleans out our little fountain pond. last year, after he did it, all of the fish were dead within a few days. that has never happened. the only thing we can think is that is had to do with him stirring up the gunk on the bottom, but he does the same thing every year. we want to avoid it happening again this spring. any suggestions? between the herrings and the mysterious cleaning deaths, we have a lot to worry about with those fish!