Chronic exposure to arsenic, primarily from groundwater sources, constitutes a major global public health concern owing to the skin lesions and cancer it can cause. Arsenic transport and retention in carbonate aquifers were investigated using an integrated combination of micro-CT, digital rock physics, and multiscale reactive transport modelling. Focusing on carbonate-rich groundwater systems of Cyprus, this study yields new insights into how pore-scale structure, hydrodynamic forcing, and solid-phase contamination history control arsenic mobilisation under pumping conditions. High-resolution micro-CT imaging was used to characterise pore geometry and generate image-based permeability maps, which were incorporated into CrunchFlow simulations transcending the pore- (μm), core- (mm), and aquifer-scale (m) scales. The simulations revealed a pronounced spatial scale dependence in arsenic behaviour. At the metre level, increasing pumping rates raised outlet arsenic concentrations from ~3.5 μg/ L, at 0.36 L/ h, to ~17.5 μg/ L, at 1,800 L /h, exceeding the World Health Organization drinking-water guideline threshold of 10 μg/ L, while adsorption 3 onto the solid matrix declined from ~39 μg to ~24 μg. Finer-scale domains exhibited substantially greater sensitivity, with aqueous concentrations approaching ~30 μg/L, which is about threefold the WHO recommendation, while retained inventories dropped ~12 μg, at high flow rates. The amount of arsenic initially stored in the rock matrix controlled the concentration of arsenic measured in groundwater. Increasing the initial amount of Ca₃(AsO₄)₂ content from 20% to 60% and 100% consistently produced higher aqueous arsenic concentrations (up to ~18%) across all spatial scales, indicating control by solid-phase availability rather than extensive mineral dissolution. Desorption-focused simulations showed rapid elevations in concentration with pumping rates, peaking near ~17.7 μg/L before reaching residence-time controlled plateaus. Long-term dilution scenarios (500 L/h over 50 years) lowered dissolved arsenic by ~20–25% but marginally tempered solid-phase inventories (≤2%), indicating that the carbonate matrix acts as a persistent but reversible arsenic sink. To assess transboundary environmental impacts, a multiphase-flow analysis of the September 2022 Nord Stream pipeline leak was conducted. The study estimated a methane release of 478,000 tonnes, making it one of the largest methane emission events in recent history. Results showed that around 63% of the total methane was released within the first 48 hours due to the high-pressure difference between the pipelines and the surrounding seawater.
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