Drought and salinity are the major abiotic stress factors negatively affecting the morphophysiological, biochemical, and anatomical characteristics of numerous plant species worldwide. The detrimental effects of these environmental factors can be seen in leaf and stem anatomical structures including the decrease in thickness of cell walls, palisade and spongy tissue, phloem and xylem tissue. Also, the disintegration of grana staking, and an increase in the size of mitochondria were observed under salinity and drought conditions. Drought and salt stresses can significantly decrease plant height, number of leaves and branches, leaf area, fresh and dry weight, or plant relative water content (RWC%) and concentration of photosynthetic pigments. On the other hand, stress-induced lipid peroxidation and malondialdehyde (MDA) production, electrolyte leakage (EL%), and production of reactive oxygen species (ROS) can increase under salinity and drought conditions. Antioxidant defense systems such as catalase, peroxidase, glutathione reductase, ascorbic acid, and gamma-aminobutyric acid are essential components under drought and salt stresses to protect the plant organelles from oxidative damage caused by ROS. The application of safe and eco-friendly treatments is a very important strategy to overcome the adverse effects of drought and salinity on the growth characteristics and yield of plants. It is shown that treatments with plant growth-promoting bacteria (PGPB) can improve morphoanatomical characteristics under salinity and drought stress. It is also shown that yeast extract, mannitol, proline, melatonin, silicon, chitosan, α-Tocopherols (vitamin E), and biochar alleviate the negative effects of drought and salinity stresses through the ROS scavenging resulting in the improvement of plant attributes and yield of the stressed plants. This review discusses the role of safety and eco-friendly treatments in alleviating the harmful effects of salinity and drought associated with the improvement of the anatomical, morphophysiological, and biochemical features in plants.