Water contamination by multiple pollutants is a serious environmental issue originating from the many diverse sources of pollution. It has worsened with the appearance of new contaminants, named emerging micropollutants, such as drug residues which are considered a potential threat to human health and/or ecosystems. These require prior treatment before release into the environment. Simultaneous adsorption and photocatalysis as well as solid-liquid separation are promising technologies for water treatment. In order to obtain low cost photoactive nanocomposites, porous and magnetic Fe3O4-hydroxyapatite (wFeHAp) nanocomposites were prepared by soft chemistry from the dissociation of natural phosphate into Ca2+ and H3PO4 precursors, further neutralized by ammonia in the presence of preformed Fe3O4 particles. The magnetic nanocomposites were characterized and examined as effective antibacterial agents. Fe3O4 association with apatite modifies the surface properties of the wFeHAp nanocomposite materials, yielding efficient antimicrobial activity for S. aureus, B. subtilis, E. coli and K. pneumoniae strains. The photocatalytic removal of ciprofloxacin (CPF) and oxytetracyclin (OXT) antibiotics in water was also evaluated. The wFeHAp nanocomposites adsorbed and degraded the selected antibiotics successfully. Toxicity evaluation of the treated water after photodegradation using the four strains demonstrates the absence of toxic by-products at the end of the reaction. Therefore, Fe3O4@HAp nanoparticles are valuable for antimicrobial and photocatalysis applications.