Describing how soil properties vary spatially is of particular importance in stochastic analyses of geotechnical problems, because spatial variability has a significant influence on local material and global geotechnical response. In particular, the scale of fluctuation θ is a key parameter in the correlation model used to represent the spatial variability of a site through a random field. It is, therefore, of fundamental importance to accurately estimate θ in order to best model the actual soil heterogeneity. In this paper, two methodologies are investigated to assess their abilities to estimate the vertical and horizontal scales of fluctuation of a particular site using in situ cone penetration test (CPT) data. The first method belongs to the family of more traditional approaches, which are based on best fitting a theoretical correlation model to available CPT data. The second method involves a new strategy which combines information from conditional random fields with the traditional approach. Both methods are applied to a case study involving the estimation of θ at three twodimensional sections across a site and the results obtained show general agreement between the two methods, suggesting a similar level of accuracy between the new and traditional approaches. However, in order to further assess the relative accuracy of estimates provided by each method, a second numerical analysis is proposed. The results confirm the general consistency observed in the case study calculations, particularly in the vertical direction where a large amount of data are available. Interestingly, for the horizontal direction, where data are typically scarce, some additional improvement in terms of relative error is obtained with the new approach.