Recent advances in using immunological and nucleic acid probes to detect the effects of environmental stress on phytoplankton growth rate and yield are reviewed here. The rationale for this approach is discussed in the context of the general response observed from microorganisms grown under stress imposed by various environmental factors. Retrenchment, or the observed down-regulation of metabolic processes under nutrient deficiency, is categorized as a general response that is of limited use in designing probes to stress induced by a specific nutrient. In contrast, compensation and the increase capacity for nutrient acquisition are specific responses that appear more promising for the development of such probes. Methods and approaches used to design immunological and nucleic acid probes for stress imposed by nutrient deficiency are reviewed. Specific examples for iron and nitrogen limitation are presented to demonstrate the potential use of nutrient stress indicators in natural populations of phytoplankton. Finally, the limitations of this approach and the importance of understanding the regulation of the genes and proteins used to prepare the probes are emphasized.