In recent years, researchers focused their attention on mesoporous silica nanoparticles (MSNs) owing to the considerable advancements of the characterization methods, especially electron microscopy methods, which allowed for a clear visualization of the pore structure and the materials encapsulated within the pores, along with the X-ray diffraction (small angles) methods and specific surface area determination by Brunauer–Emmett–Teller (BET) technique. Mesoporous silica gained important consideration in biomedical applications thanks to its tunable pore size, high surface area, surface functionalization possibility, chemical stability, and pore nature. Specifically, the nature of the pores allows for the encapsulation and release of anti-cancer drugs into tumor tissues, which makes MSN ideal candidates as drug delivery carriers in cancer treatment. Moreover, the inner and outer surfaces of the MSN provide a platform for further functionalization approaches that could enhance the adsorption of the drug within the silica network and the selective targeting and controlled release to the desired site. Additionally, stimuli-responsive mesoporous silica systems are being used as mediators in cancer therapy, and through the release of the therapeutic agents hosted inside the pores under the action of specific triggering factors, it can selectively deliver them into tumor tissues. Another important application of the mesoporous silica nanomaterials is related to its ability to extract different hazardous species from aqueous media, some of these agents being antibiotics, pesticides, or anti-tumor agents. The purpose of this paper is to analyze the methods of MSN synthesis and related characteristics, the available surface functionalization strategies, and the most important applications of MSN in adsorption as well as release studies. Owing to the increasing antibiotic resistance, the need for developing materials for antibiotic removal from wastewaters is important and mesoporous materials already proved remarkable performances in environmental applications, including removal or even degradation of hazardous agents such as antibiotics and pesticides.