Cyanobacteria are equipped with numerous mechanisms that allow them to survive under conditions of nutrient starvation, some of which are unique to these organisms. This review surveys the molecular mechanisms underlying acclimation responses to nitrogen and phosphorus deprivation, with an emphasis on non-diazotrophic freshwater cyanobacteria. As documented for other micro-organisms, nutrient limitation of cyanobacteria elicits both general and specific responses. The general responses occur under any starvation condition and are the result of the stresses imposed by arrested anabolism. In contrast, the specific responses are acclimation processes that occur as a result of limitation for a particular nutrient; they lead to modification of metabolic and physiological routes to compensate for the restriction. First, the general acclimation processes are discussed, with an emphasis on modifications of the photosynthetic apparatus. The molecular mechanisms underlying specific responses to phosphorus and nitrogen-limitation are then outlined, and finally the cross-talk between pathways modulating specific and general responses is described.