Investigation of Larval Fish Communities in Shallow and Tidal Marsh Habitats of the Upper San Francisco Estuary: Insights Gained from Sampling Uncharted Waters

An understanding of the factors that affect the recruitment of larval fish partially hinges upon a robust temporal and spatial monitoring program.  We sampled larval fish in shallow and tidal marsh habitats in the low salinity region of the San Francisco Estuary to get a better understanding of the value of these overlooked habitats for fish and zooplankton. Larval fish were sampled from February to June in 2013 and 2014 using a 505 µm mesh net towed from the stern of a small boat. Zooplankton and water quality (salinity, turbidity, DO, PH, Chl a) were sampled concurrently to determine what factors affected abundance and distribution of key fish species. Overall, pacific herring (Clupea pallasii), longfin smelt (Spirinchus thaleichthys), prickly sculpin (Cottus asper), and pacific staghorn sculpin (Leptocottus armatus) were the most abundant species collected during the study. Year-to-year differences were observed for most species, which was largely attributable to different regional salinity dynamics.  Within year differences were mostly influenced by water temperature. Our study suggests that shallow bays and tidal marshes provide suitable rearing habitat for many key species of management interest.