Natural disasters disrupt maritime operations, yet their environmental consequences remain underexplored. This study quantifies CO₂ emission changes following the February 2023 İskenderun Bay earthquakes (Mw 7.7 and 7.6) using AIS-derived port visit data and graph neural network modeling. Analyzing 25,837 port visits across a 36-month period (January 2022–December 2024), we compared emissions during baseline (pre-earthquake), acute disruption (February–June 2023), and recovery phases. Results revealed a statistically significant 35.9% increase in per-visit CO₂ emissions during the acute phase (t = 11.79, p < .001, Cohen's d = 0.27), driven by extended port visit durations (from 77.87 to 105.82 hours). Counterfactual analysis estimated 27,574 tonnes of excess CO₂ emissions directly attributable to earthquake disruption. Network analysis showed 23.8% reduction in edge density during the acute phase. The Temporal Graph Attention Network model achieved R² = 0.985 (baseline) and R² = 0.997 (recovery) in predicting emission patterns, while acute phase showed predictability collapse (R² = −1.591). These findings demonstrate that seismic events generate significant environmental externalities beyond immediate physical damage, with implications for disaster preparedness, port resilience planning, and maritime emission accounting under frameworks such as the EU MRV Regulation.