The understanding of the spatio-temporal variability of the red squat lobster (Pleuroncodes monodon), according to the water masses of the Peruvian Sea, is limited despite the key role this crustacean plays in the trophic chain of the epipelagic community offshore Peru. This study aims to investigate the spatio-temporal fluctuations of the distribution and abundance of this species in function of the dynamics of the Peruvian sea superficial water masses. Hydroacoustic and oceanographic data sets acquired during 56 fisheries assessment cruises by the Peruvian Sea Institute (IMARPE) between 1998 and 2016 were used in this study. Through cross-correlation analysis (CCA) we compare the time series of the occupied area (OA), the center of gravity (CG) and the average acoustic density (sA+) of red squat lobster population with the time series of the occupied area and average distance from the coast of each water mass. In addition, a preference index (wmPREF) was derived to examine the degree of association between the red squat lobster and each water mass. Results show that the red squat lobster exhibit three behaviors according to the superficial water masses of the Peruvian Sea: (1) a positive association with the Cold Coastal Waters (CCW), (2) a neutral association with the Mixed Waters (MWCS), (3) a negative association with the Subtropical Superficial Waters (SSW). The ACC demonstrates that when CCW contracts, MWCS expands and SSW gets close to the coast, red squat lobster's sA+ increase, OA decrease and CG move to the coast and to the south. In contrast, when CCW expands, MWCS contracts and SSW moves away from the coast, sA+ decrease, OA increase and CG move to the west and to the north. From that results, we interpret that the CCW constitutes a favorable habitat for the distribution of this crustacean. We conclude that the red squat lobster follows the habitat-based hypothesis in the Peruvian Sea which points out that fluctuations of a population are linked to the variations of its favorable habitat.