This work analyses the interaction of autonomous underwater vehicles (AUVs) with certain aspects of the ocean variability. Specifically, a simplified dynamical model of an AUV is integrated in ocean environments showing certain spatial variability. The length scales of the spatial structures are different for each environment and range from scales similar to the AUV to a hundred times bigger. Results indicate that the perturbations induced on the AUV by the environmental variability are stronger in the cases where the ocean structures are of similar size than the AUV. The strength of the perturbation decreases if the length scale of the spatial variability is increased. It was found that the perturbations induced by the environment on the AUV, are characterized by a power spectrum peaked at wavelengths of the typical eddy size.