Temperature is a useful environmental tracer for quantifying movement and exchange of water and heat through and near sediment–water interfaces (SWI). Heat tracing involves analyzing temperature time series or profiles from temperature probes deployed in sediments. Ex-Stream is a MATLAB program that brings together two transient and two steady one-dimensional coupled heat and fluid flux analytical models. The program includes a graphical user interface, a detailed user manual, and postprocessing capabilities that enable users to extract fluid fluxes from time-series temperature observations. Program output is written to comma-separated values files, displayed within the MATLAB command window, and may be optionally plotted. The models that are integrated into Ex-Stream can be run collectively, allowing for direct comparison, or individually.