Their principal food item is the opossum shrimp, Neomysis mercedis, and species of Acanthomysis, but they will also eat copepods and other small crustaceans.

In turn, they are eaten by a variety of fishes, birds, and marine mammals; for instance, they are an important prey for the harbor seal, Phoca vitulina, in the Columbia River.

The longfin smelt have been primarily affected by import and export of water from these estuaries, resulting in high mortality rates.

The recent conversion of salt ponds into the tidal marsh combined with low salinity, nutrient-rich effluent recycled water from the San Jose-Santa Clara Regional Wastewater Facility may be supporting an important previously unknown source population of longfin smelt.

Given past abundance in the San Francisco Bay estuary, longfin smelt were likely historically an important forage fish, but have declined 99.9% from pre-1980's levels.