Managing lake eutrophication requires a clear understanding of resource limitation of primary productivity, yet historically research on this subject has focused on temperate lakes. In 2010, we quantified several metrics of resource limitation in Lake Atitlán, Guatemala, Central America’s deepest tropical mountain lake that has recently experienced extensive phytoplankton blooms. In contrast to many temperate lakes, Lake Atitlán did not show a relationship between total phosphorus (TP) and chlorophyll a (Chl-a) concentrations. Average molar ratios of total nitrogen (TN) to TP decreased from 16.4 to 4.5 between stratified and mixing conditions. During our monitoring period, Tropical Storm Agatha landed on Guatemala, washing in sediment from the watershed, and concentrations of P temporarily increased in the lake by >60%. Initial experimental bioassays indicated phytoplankton growth was colimited by N and P prior to the storm, whereas post-storm assays suggested limitation by P and trace elements. Compared to previous years, Limnoraphis robusta, an N-fixing cyanobacterium, increased in abundance earlier in the year; however, there was no bloom event during our sampling period. Experimental studies indicated that nitrogenase activity was limited by P and iron availability while light was secondarily limiting of overall phytoplankton growth. This study illustrates the potential for baseline nutrient and phytoplankton growth dynamics to substantially differ for tropical lake systems from conventionally studied temperate lakes and the potential for “pulse” events (e.g., tropical storms) to alter those dynamics