Magnetite-based nanocomposites are used for biomedical, industrial, and environmental applications. In this study, we evaluated their effects on survival, malformation, reproduction, and behavior in a zebrafish animal model. Nanoparticles were synthesized by chemical coprecipitation and were surface-functionalized with (3-aminopropyl) triethoxysilane (APTES), L-cysteine (Cys), and 3-(triethoxysilyl) propylsuccinic anhydride (CAS). All these nanocomposites were designed for the treatment of wastewater. Zebrafish embryos at 8 h post-fertilization (hpf) and larvae at 4 days post-fertilization (dpf) were exposed to the magnetic nanocomposites Fe3O4 MNP (magnetite), MNP+APTES, MNP+Cys, MNP+APTES+Cys, and MNP+CAS, at concentrations of 1, 10, 100, and 1000 µg/mL. Zebrafish were observed until 13 dpf, registering daily hatching, survival, and malformations. Behavior was tested at 10 dpf for larvae, and reproduction was analyzed later in adulthood. The results showed that the toxicity of the nanocomposites used were relatively low. Exploratory behavior tests showed no significant changes. Reproduction in adults treated during development was not affected, even at concentrations above the OECD recommendation. Given the slight effects observed so far, these results suggest that nanocomposites at the concentrations evaluated here could be a viable alternative for water remediation because they do not affect the long-term survival and welfare of the animals.