Abstract Fourier Transform Infrared (FT-IR) microspectroscopy provides an in situ, nondestructive chemical analysis of individual algal cells. Algae play key roles in nutrient cycling and energy flow through aquatic ecosystems and are pivotal in the sequestration of inorganic nutrients (e.g., carbon, nitrogen, and phosphorus) and transformation into organic forms. However, most methods used to measure algal nutritional and physiological changes are limited to detecting whole community responses because of the relatively large quantity of material needed for analysis (i.e., milligrams to grams). The spatial resolution achievable with infrared microspectroscopy allows for the analysis of macromolecular pools (e.g., proteins, lipids, carbohydrates) in individual cells that allows species specific measurements within heterogeneous microscopic communities. Initial applications characterized molecular pools within marine macroalgae and have since progressed toward ecologically based questions concerning algal physiological responses to changing nutrient availability in marine and freshwater ecosystems.