Fish kills are reported throughout the nation and a great deal of research is conducted in an attempt to determine the cause of these mortality events. Low dissolved oxygen concentrations, eutrophication, and/or harmful algal blooms are most commonly cited as causative factors. Lake Madeline and Offatt's Bayou on Texas' upper coast have low mixing environments due to their relatively small areal size, deep basins, small tidal inlets, and restricted exchange with the nearby Galveston Bay estuary complex. These physical attributes, along with near annual fish kills, make them an ideal study area for understanding the causes and effects of hypoxia and phytoplankton blooms on fish kills. We measured physical, chemical, and biological parameters twice weekly over the course of two summers. Fortuitously, a fish kill occurred in the summer of 2005 but not in 2006, which allowed us to narrow down the likely contributing factors that led to the kill, consisting of >10,000 Brevoortia partonus (Gulf menhaden). Large amounts of detritus from a cyanobacterial bloom, in conjunction with the strong stratification and hypoxic bottom waters, led to the fish mortality event in 2005. While the system was also stratified during the summer of 2006, chlorophyll and phaeophytin concentrations were 15-fold lower and no fish kill was observed. The combination of factors that led to the observed fish kill demonstrates the importance of interdisciplinary approaches to investigating the causes of ecological disturbances.