Graphene oxide (GO) and their natural/synthetic composites are encouraging tools for humanity. There is a need to address critical challenges and potential risk possibilities in GO-based architectures, which have a wide range of uses. In this study, ecotoxicological levels as well as GO-based nanoparticle synthesis, characterization, interaction mechanism and toxicity detection levels for potential biomedical applications were determined on zebrafish (Danio rerio). The effects of GO-ED-BA NP (graphene oxide-boramidic acid nano particles) which was characterized by FT-IR, SEM, TEM, and BET on survival rate, morphological abnormalities (yolk sac edema, lordosis/kyphosis, pericardial edema, and tail malformation), hatching rate as well as neuronal degeneration /necrosis, 8 OHdG and TNF-alpha expression were observed in D. rerio embryos and larvae. In the obtained findings, it was determined that the toxicity profile of GO-ED-BA NP appeared similar, in high-dose application with single GO use, causing a cytotoxic, pro-inflammatory response and triggering oxidative stress. However, increased malformation rates and mortality at the highest concentration were due to nanoparticle sizes and GO. The presence of boramidic acid unit on graphene nanostructure changed the GO's toxicity profile and positively directed the proinflammatory and oxidative stress response. Synthesizing of graphene oxide-boramidic acid and its toxicity panels compared to graphene oxide are reported for the first time in this study.