Abstract Under the present changing climate conditions and the observed temperature increase, it is of high importance to understand its effects on aquatic microbial life, and organisms’ adaptations at the biochemical level. To adjust to temperature or salinity stress and avoid cell damage, organisms alter their degree of fatty acids (FAs) saturation. Thus, temperature is expected to have strong effects on both the quantity and quality of FAs in aquatic microorganisms. Here we review some recent findings about FAs sensitivity to climate change in contrasting environments. Overall, heat waves may induce changes in the relative abundance of polyunsaturated FAs (PUFA). However, the impact of the exposure to warming waters is different in temperate and polar environments. In cold marine waters, high concentration of omega-3 (ω3) FAs such as eicosapentaenoic acid (EPA) is promoted due to the activation of the desaturase enzyme. In this way, cells have enough energy to produce or activate antioxidant protection mechanisms and avoid oxidative stress due to heat waves. Contrastingly, under high irradiance and heat wave conditions in temperate environments, photosystems’ protection is achieved by decreasing EPA concentration due to desaturase sensitivity. Essential FAs are transferred in aquatic food webs. Therefore, any alteration in the production of essential FAs by phytoplankton (the main source of ω3) due to climate warming can be transferred to higher trophic levels, with cascading effects for the entire aquatic ecosystem.