LOS ANGELES — The City Council has approved an agreement between the Harbor Department and several government agencies that calls for the restoration of the Batiquitos Lagoon in San Diego County in exchange for state permission to build a landfill in San Pedro Bay. The agreement requires the Port of Los Angeles to restore the polluted estuary--at an estimated cost of $20 million--as compensation for the loss of marine life when the port creates a 450-acre landfill in Los Angeles Harbor. State officials, who worked out the agreement, chose the Batiquitos Lagoon because they said they were unable to find an acceptable restoration project in the Los Angeles area. Port officials said they expect the City of Carlsbad, site of the 526-acre lagoon, to approve the agreement Tuesday. The port is conducting engineering studies at the lagoon, but restoration is not expected to begin until 1989.