The La Jolla Agreement established the International Dolphin Conservation Program (IDCP) which sought to reduce the take of dolphins to levels approaching zero and established a schedule of dolphin mortality limits which progressively reduced the limits on the number of dolphins that could be caught each year until 1999, when the number was to be less than 5,000 dolphins. The total limits on dolphin mortality were then divided into individual Dolphin Mortality Limits (DMLs), and distributed to the parties to the Agreement in proportions relating to the number of vessels wishing to participate in the fishery, and meeting certain requirements, under their jurisdiction. Vessels were not permitted to exceed the limits set for them, otherwise they would receive correspondingly reduced allocations in subsequent years. In addition, the program established: a comprehensive observer programme; a review panel to monitor and report on compliance with the limits set; and a scientific advisory board to facilitate and guide research on reducing dolphin mortalities, and in particular to advise on how purse seine technology could be modified to make it less likely to cause dolphin mortality.

Although some concerns were expressed about levels of compliance under the agreement (flowing from its voluntary nature), the operation of the Agreement was highly successful and exceeded expectations, with the final year target of less than 5,000 dolphin deaths being achieved in the first year. By 1998, annual dolphin mortality had dropped to below 2,000. The IDCP continues to operate in the Eastern Pacific Ocean, although it now operates under the 1998 Agreement on the International Dolphin Protection Program, which is a binding international agreement based on (but extending) the La Jolla Agreement.