There is a great concern about the impacts of climate changes namely due to salinity seawater and temperature alterations in aquatic organisms with the estuarine and coastal environments being the major affected areas. The intensive usage of chemicals in an indiscriminate way in agriculture practices, achieving, in some cases, values above the limits of contamination authorized by the European legislation, also drastically affects the surrounded estuarine areas with profound consequences to the water quality and the aquatic communities. It is known that stressors affect organisms' physiological conditions with recent works concerning alterations in the fatty acid (FA) profiles associated with environmental and contamination events that become more frequent. FA plays a key role in immune and physiological functions and is associated with the prevention of some diseases, shown to be good bio-indicators to assess the organisms' impacts under stress conditions. Thus, this chapter proposes to address natural (salinity and temperature) and chemical (herbicide and metal) stressors' impacts in the FA profiles of Thalassiosira weissflogii and Cerastoderma edule and infers about the effects on organisms' physiological processes and along the food web. Consequences in food resources and to healthier and nutritious food consumption with benefits to human beings are also assessed.