Upwelling has profound effects on nearshore tropical ecosystems, but our ability to study these patterns and processes depends on quantifying upwelling dynamics in a repeatable and rigorous manner. Previous methods often lack the ability to identify individual cold-pulse events within temperature time series data or require several user-defined parameters, and therefore previous hydrographic knowledge of the study site. When unavailable, parameters are chosen arbitrarily or from previous studies potentially conducted under different environmental contexts. Previous methods also require the user to manually separate upwelling-induced cold-pulse events from those caused by other physical mechanisms like surface downwelling. Here, we present a novel method that uses a temperature stratification index (TSI) to detect upwelling-induced cold-water intrusions in tropical waters. We define a cold pulse as a continuous period having an abnormally low TSI, with this criterion based on a climatological threshold of the temperature profile at the study site calculated from the National Centers for Environmental Prediction's Global Ocean Data Assimilation System (GODAS) reanalysis product. Our TSI method is therefore automatically tuned for the study site in question, removing biases associated with user-defined input parameters. The method also automatically determines the directional origin of the cold-water mass to isolate upwelling-induced cooling and can achieve overall cold-pulse detection rates 10–14.2% higher than previous methods. Our new TSI method can easily be adapted to detect a range of physical processes in shallow waters, including intrusion of water masses through upwelling, downwelling, and horizontal advection.