A recent decline of fall-run Chinook salmon (Oncorhynchus tshawytscha) abundance within the Klamath Basin has led to the near-complete closure of Chinook salmon fisheries along the coast of California during the 2006 season. These populations, however, are affected not only by fisheries but also by river and ocean conditions, making the management of these populations extremely complex. Here, we present a comprehensive analysis of annual spawning-adult counts of Chinook salmon at multiple locations in the Klamath River and its tributaries over the period of 1978 to 2005. Treating the data as multivariate time-series data, we identified three smooth trends affecting the population. A further analysis was undertaken to associate these trends with environmental indices that represent six broad categories of physical/biological conditions. This analysis revealed that the trends are strongly associated with indices representing the stream flow rate, the coastal upwelling, and large-scale ocean condition. The timing of associations between the number of spawning adults and the environmental indices suggests that the environmental conditions experienced by a cohort during their early life stage as well as by their parents prior to spawning are important in determining the abundance of future returns. These results suggest that salmon populations are influenced by multiple environmental factors affecting various life-stages of individuals.