Estuarine fish and invertebrate assemblages at Tijuana Estuary and Los Penasquitos Lagoon exhibited changes coincident with the 1997-1998 El Nino event. Three fishes [Albula sp. (bonefish), Ctenogobius sagittula (longtail goby) and Acanthogobius flavimanus (yellowfin goby)] and three invertebrate species [Callinectes arcuatus (arched swimming crab), Penaeus californiensis (Mexican brown shrimp), and Petricola hertzana (bivalve)] were new to estuary monitoring records. In addition, three historically common species exhibited substantial changes in abundance and/or size frequency: Mugil spp. (mullet spp. ), Grandidierella japonica (amphipod), and Tagelus californiensis (jackknife clam). Likely mechanisms for the observed patterns include modified ocean currents, altered larval supplies, increased rainfall, and flooding disturbance. Long-term biological monitoring programs (12-yr) provided valuable baseline data for quantifying these changes and recording faunal patterns over interannual-decadal time scales.