Consider doing homework on microbial / bacterial additions in your case pelleted types on your mucky shoreline areas before you invest in liner and sand/gravel reconstruction. Be aware not all pelleted bacteria are the same - some good, some not so good. Kevin Ripp the Bug Man at Aquafix Inc advertises here and speaks at the Pond Boss Conferences. His pelleted bacteria formulations are proven muck eaters.
I have found that manual raking of beach areas with and without bacteria additions work wonders to reduce muck in shallow beach areas. Check into a Lake Rake and add a 3ft piece of 1/2" rebar rod for additional weight and raking - tilling benefits. Weekly or twice weekly raking does wonders for reducing muck in beach areas with sand or gravel substrates.
Here is a link that I found for Kevin Ripp's group Aquafix who is an advertiser here on PBoss.
http://www.teamaquafix.com/
