Magnetic nanocomposite sorbents are increasingly explored for the remediation of metal-contaminated waters; however, high abiotic removal efficiency may not always translate into biological safety. The present study evaluated the single and combined effects of dissolved cobalt (II) ions and magnetite–chitosan nanocomposites (MCN) in zebrafish (Danio rerio) embryos and larvae. MCN (30 wt.% Fe₃O₄) were synthesized via co-precipitation and crosslinking and physiochemically characterized. Adsorption experiments conducted in fish incubation medium demonstrated the efficacy of divalent Co removal and were well described by the Langmuir isotherm model, with a maximum experimental capacity of 20.08 mg g⁻¹. The biological endpoints encompassed survival, hatching, heart rate, locomotor behavior, and oxidative stress biomarkers in early-stage zebrafish. The presence of cobalt (II) was found to result in a reduced hatching success rate, the induction of persistent bradycardia, and the occurrence of oxidative stress, as evidenced by a decline in SOD activity and an increase in H₂O₂ and MDA levels. The study found that MCN alone did not lead to mortality or increase peroxide levels or lipid peroxidation, although a modest decrease in SOD activity was observed. In contrast, combined exposure to cobalt and MCN resulted in significant delayed mortality (>85% at 96 h) and early neuromotor impairment. These findings indicate that high abiotic sorption efficiency alone does not guarantee reduced biological toxicity when nanomaterial–metal interactions occur. Consequently, safety assessments of remediation nanomaterials should explicitly consider nanomaterial–metal interactions and developmental stage-specific biological responses.