In the French West Indies, the chlordecone (organochloride pesticide) pollution is now diffuse becoming new contamination source for crops and environment (water, trophic chain). Decontamination by bioremediation and chemical degradation are still under development but the physical limitations of these approaches are generally not taken into account. These physical limitations are related to the poor physical accessibility to the pesticides in soils because of the peculiar structural properties of the contaminated clays (pore volume, transport properties, permeability, and diffusion). Some volcanic soils (andosols), which represent the half of the contaminated soils in Martinique, contain nanoclay (allophane) with a unique structure and porous properties. Andosols are characterized by pore size distribution in the mesoporous range, a high specific surface area, a large pore volume, and a fractal structure. Our hypothesis is that the clay microstructure characteristics are crucial physico-chemical factors strongly limiting the remediation of the pesticide. Our results show that allophane microstructure (small pore size, hierarchical microstructure, and tortuosity) favors accumulation of chlordecone, in andosols. Moreover, the clay microporosity limits the accessibility of microorganisms and chemical species able to decontaminate because of poor transport properties (permeability and diffusion). We model the transport properties by two approaches: (1) we use a numerical model to simulate the structure of allophane aggregates. The algorithm is based on a cluster–cluster aggregation model. From the simulated data, we derived the pore volume, specific surface area, tortuosity, permeability, and diffusion. We show that transport properties strongly decrease because of the presence of allophane. (2) The fractal approach. We characterize the fractal features (size of the fractal aggregate, fractal dimension, tortuosity inside allophane aggregates) and we calculate that transport properties decrease of several order ranges inside the clay aggregates. These poor transport properties are important parameters to explain the poor accessibility to pollutants in volcanic soils and should be taken into account by future decontamination process. We conclude that for andosols, this inaccessibility could render inefficient some of the methods proposed in the literature.