Fish are an essential part of the wetland food chain because of their role in nutrient cycling and because, as prey items, they have the potential to transfer energy from a marine environment to a terrestrial environment. This is especially important at Los Peñasquitos Lagoon, where fish are prey to endangered birds such as the California least tern and the light-footed Ridgway’s rail.

Because of its history of periodic inlet closures and sewage spills, the fish assemblage at the Lagoon fluctuated in terms of diversity and relative abundance. Inlet closure during warm periods led to rapid deterioration of water quality and resulted in mortality of fishes, sometimes on a massive scale. Once the inlet opened naturally or was opened mechanically, fish eggs, larvae, juveniles, and adults recruited from the shallow nearshore habitat and prospered in the Lagoon until the inlet closed again. With inlet management by LPLF, fish populations have become more stabilized. Sewage spills in the Lagoon have also contributed to periodic large-scale fish kills as DO quickly dropped to toxic levels. The most recent occurrence happened on September 9, 2011, during a region-wide power failure that resulted in an estimated 2.3 million gallons of raw sewage discharged just upstream of the Lagoon; widespread fish kills were documented by CSP and the San Diego Coastkeeper.

Monitoring efforts at Los Peñasquitos Lagoon have detected the numerous species that include:

Much like fish, benthic invertebrates are essential to wetlands because of their role in nutrient cycling and because, as prey items, they also have the potential to transfer energy from a marine environment to a terrestrial environment. They are especially important prey items for migratory and resident shorebirds.

Monitoring efforts at Los Peñasquitos Lagoon have detected the numerous species that include: