Several species of the diatom genus Thalassiosira Cleve, were observed in freshwater phytoplankton samples collected from a fifty-two kilometer reach of the San Joaquin River in the vicinity of Stockton, California, USA. The study was conducted between the South Airport Way bridge near Vernalis and the Stockton Deep Water Ship Channel during fall and summer of both 2005 and 2006. The entire reach is freshwater habitat with the lower twenty-eight km strongly influenced by tidal flow reversals driven by the San Francisco Estuary. Ninety four whole water samples were collected from surface waters during the months of July, August, September and October in 2005 and the months of July and August in 2006. Six species of Thalassiosira were identified using scanning electron and light microscopy: T. weissjlogii (Grunow), T. gessneri Hustedt, T. lacustris (Grunow), T. visurgis (Grunow), T. decipiens (Grunow), and T. incerta (Makarova). Of the species observed, only T. weissjlogii has been previously reported in the freshwater portion of the San Joaquin River. The other five species have been previously reported from sites in the San Joaquin- San Francisco Estuary characterized as brackish, suggesting they are distributed in waters of various salinities ranging from freshwater to brackish within the river and estuary.

A molecular system was developed and tested to efficiently analyze algal communities in river water samples. Polymerase Chain Reaction (PCR) primers were designed to amplify the 18S rRNA gene of certain taxonomic groups of freshwater algae; there was limited success in specific amplification. Additionally, a primer pair utilizing both the 16S plastid gene and the 16S rRNA gene was tested with success, amplifying both prokaryotic and eukaryotic algae while excluding other taxonomically similar organisms. The terminal restriction fragment length polymorphism (TRFLP) fingerprinting method, which has been used in previous studies to examine prokaryotic community structure, was modified with the successful algae primers to selectively fingerprint all algal groups in two San Joaquin River water samples. Triplicates of two TRFLP profiles have been generated and terminal restriction fragments (TRFs) have been assigned to specific algal species.

This thesis is a history of the navigation on the San Joaquin River from 1848 until 1925. The main purpose of the thesis will be to examine chronologically any and all events and factors concerned with the navigation of the river during that period of time. The first chapter will survey the geographical and historical background of the San Joaquin River. The emphasis will be placed on the river's use for navigation. Since the upper, southern third of the San Joaquin Valley does not drain into the San Joaquin River, only those areas between the Kings River on the south and the Cosumnes River on the north will be included in this study.