According to the California Department of Fish and Game, the official state regulatory agency for Batiquitos Lagoon, fishing is allowed in the Lagoon from the shore but only from designated sites. Walking through the marsh or nesting areas is not allowed. Since there are no trails designated for fishing, there are only two areas from which fishing is allowed:
From the rock jetties at the mouth, and
From the rocks under Interstate-5 (east or west of the freeway, on the north side only).
Boats are not allowed, and, therefore, fishing from boats is not allowed.