Estuaries connect freshwater and ocean environments for Pacific salmon, providing important habitats during a crucial transition period for juveniles. Juvenile Pacific salmon from all five species migrate through the Fraser River estuary, British Columbia, annually, but little is known about estuary residence or habitat preferences of different populations. The Fraser estuary continues to support juvenile salmon, the vast majority of habitat which once existed has been lost, and estuary connectivity is highly altered by jetties and causeways. We have conducted an extensive juvenile salmon research program throughout the Fraser River delta over the last four years (2016-19), surveying salmon at 36 sites that encompass three habitat types using beach and purse seine, and fyke net methods. We have captured over 13,000 juvenile salmon including 5,015 juvenile Chinook and 7,962 juvenile chum and have collected 2,127 tissue samples from Chinook for genetic stock identification. We found that the Fraser estuary supports juvenile salmon from throughout the watershed and across four species including sub yearling Chinook, chum, pink and sockeye. Outmigration timing and relative species abundance are similar to historical data, with juvenile Chum showing the highest abundance and juvenile Chinook showing the longest estuary residence. Ocean-type Chinook from the Harrison River are the most estuary dependent population in the Fraser, arriving around the end of March and present until mid-July, with individuals increasing in size over the season, and otolith microchemistry indicating estuarine growth. Conversely, ocean-type Chinook from the South Thompson population arrive in late May or early June, at larger sizes and were last detected in mid-August. We have found that juvenile salmon mostly utilize marsh habitats, with relatively few captured in eelgrass habitats, potentially related to the presence of a large causeway altering connectivity to these productive habitats. We will also discuss how this research provides insight into potentially restoration targets and actions and how estuary reliance varies between species and populations.