We use the spatial autocorrelation (SPAC) method with improved inversion algorithms to estimate the Love and Rayleigh dispersion curves at two sites at the West and Northeast flanks of Arenal volcano, Costa Rica. At the West flank site, the Rayleigh waves phase velocities vary from 765 m s− 1 at 1 Hz to 300 m s− 1 at 12 Hz and those of Love waves between 780 and 295 m s− 1 in the same frequency band. At the Northeast flank site, the Rayleigh wave velocities range from 1386 to 300 m s− 1 and those of Love from 1983 to 315 m s− 1. From dispersion curves we derive shallow (< 400 m) P and S waves velocity models. 2D velocity models down to a depth of 150 m are also obtained by seismic refraction surveys along two radial profiles on the tephra apron at West and East flanks. They present strong vertical and lateral variations in the velocity and thickness of the layers. Strong variations in amplitude of the spectral peaks are observed for the seismic events along two radial arrays. These site effects are analysed using the H/V spectral ratio method and S-wave theoretical transfer functions. Results show that the wave amplifications are related to resonance effects of shallow structure (< 150 m) and occur only where impedance contrast with the deeper layers is strong enough. In contrast, almost no site effect are detected at the Masaya shield volcano, Nicaragua, where the structure is more homogeneous and mainly composed of lava flows. When a resonance of the shallow layers occurs, the correlation coefficients between close stations increase at the corresponding frequency. The site effects may thus produce spurious results with the SPAC method. The H/V spectral ratio, used in complement of the SPAC method, can help detecting the site effects and testing the plane layer hypothesis. Furthermore, the theoretical transfer functions calculated for the estimated velocity models is also useful to validate the models.