We estimated site effects of the earth dam El Infiernillo, located between the states of Guerrero and Michoacan, Mexico. We analyzed 125 strong-motion records from stations located at three different levels of the dam (80, 120, and 180 m) and in the free field. The selected earthquakes are located in the Cocos–North America subduction zone, with magnitudes between 3.8 and 7.9 and epicentral distances that range between 18 and 433 km. We used three methods to estimate the characteristic frequency of vibration (fn) of the recording sites. First, we calculated spectral ratios between the horizontal and the vertical components of motion (H/V ratios). Second, we estimated fn calculating standard spectral ratios using a free-field station as a reference site. Finally, we made a third estimate using cross-spectral ratios. We found that although the three methods give consistent estimates of fn, on average the H/V ratio gives more stable estimates. The H/V ratios, however, subestimate the site amplification at low frequencies (f < 8 Hz) at the top and middle sites. We suggest that this result is due to the lateral heterogeneity of the structure that favors wave-field propagation in the vertical direction.