The former Leyton Orient, Dover and AFC Wimbledon midfielder guided the club a top seven finish.
But will will not be staying with the Beachboys next season.
A club statement read: “Unfortunately Sammy has been asked to step down as first team manager due to ongoing personal problems.
“We would like to take this opportunity to wish him all the best for the future.
“Jack Midson, Darren Beale, Danny Scopes and Adam Drewe have been asked to remain at the club.
“We await their decisions and further news will be released later this week.”