The patented EDI ATLAS-IS (internal separator) system uses a biological solids separator module and “equilibrium” solids management design to provide advanced treatment in a lagoon-based wastewater treatment system. Conventional lagoon treatment systems that are experiencing hydraulic or organic overload; inadequate BOD or TSS reduction; poor ammonia conversion; high effluent total nitrogen; or reduced cold weather performance will benefit from the application of the ATLAS-IS system.