Water does look good. Time to add more structure if needed. Some new water might help reduce any water quality issues. Remember that the fish still there are operating in much less vol of water until refill.
i never really wanted any cover much for the bg. i wanted to keep the reproduction rates down with bass predation. i am kinda thinking i may need to add some cover for some of the little ones in there to hide. these warm evening have the bass in high gear. they are wearing the 1-2" bg out.
also i have a really good stream below my pond with an electric pump. i used it to top it off during a dry summer of 2017 and then i put it on a timer in 2018 to run a few hours about dark. that was my aeration-cool water blasting in. i took a sample of that water today also, just to make sure it was pure. there is no ag runoff at all upstream. the closest house is about half mile or more away through the woods. i had winterized the pump, but i started it back up today to help fill the pond for the reason you stated. also, i have a good flow of water coming in the from the stream that feeds the pond.