Within the Gulf of California, the Midriff Islands Region (MIR) is characterized by mixing conditions of water masses that lead to high primary productivity, which fosters the presence of sardines, anchovies, and their predators. Using acoustic tools, we analyzed the presence and characteristics of schools detected in three surveys carried out in late spring of 2012 and 2013 and early summer of 2014. We sought to relate changes in the geographical distribution of schools with Sea Surface Temperature (SST) and Net Primary Productivity (NPP). The largest number of schools was observed in 2012, coinciding with the highest and most extensive NPP, while the following years were associated with lower NPP coupled with a lower number of detections. During the study period, the Ballenas-Salsipuedes Channel and its area of influence showed the lowest SST and higher NPP even toward the summer as compared to the rest of the MIR, favoring the presence of fish schools and supporting the importance of this site as a feeding center for these species. As for their vertical distribution, it was found that during the day schools reach greater depths, while during the night these are concentrated in surface waters. However, no differences in size, density, or other characteristics were detected either between periods or between years. Finally, we found a high proportion of schools during the night (61%), which departs from the typical nocturnal dispersal behavior described for similar species in other areas.