The Humboldt Current System (HCS) is dominated by two pelagic species; Peruvian anchovy or anchoveta (Engraulis ringens) and sardine (Sardinops sagax). Using data from 43 acoustic surveys conducted from 1983 through 2005 by the Peruvian Marine Institute (IMARPE), we examined the distribution of these two species relative to water masses. We tested the hypothesis that anchovy was found more frequently in upwelled cold coastal water (CCW) and mixed waters (MCW) than in other water types and that sardine was more associated with more offshore oceanic surface subtropical water (SSW). Surface temperature, salinity, latitude, season and distance to the coast data were used to define water masses. Results using generalized additive models (GAM), modelling sardine and anchovy presence-absence as a function of year, water body, bottom depth and latitude, showed that anchovy were primarily found in CCW and MCS, while sardine were more ubiquitous relative to water masses with some predilection for SSW. These results were supported by various indexes of anchovy and sardine distribution versus water mass as well as temporal and location variables. © 2008 Elsevier Ltd. All rights reserved.