The world tuna fishing fleet is dominated by purse seine boats. Purse seine sets are sometimes unsuccessful in capturing fish; these unsuccessful attempts are known as null sets. Null sets have been widely documented and the numbers indicate that they happen in large proportions. In Mexico, the tuna fishery represents the second most important fishery by volume and value. The frequency of occurrence of null sets during the period 2000–2013 was analyzed to identify the regions, periods, and oceanographic conditions (e.g., ENSO) related to them. Null sets on free-swimming fish schools and between June and July had a higher relative representation. The region with highest relative occurrence was the mouth of the Gulf of California (between August and October). A positive correlation was observed between the occurrence of null sets on free-swimming fish schools and the Multivariate El Niño Index. The maximum values of occurrence of null sets were related to those months in which the water column structure presented changes. Comprehension of this phenomenon (null sets) and its relation to natural events is of importance for the fishery, as there could be repercussions for the economy and management of the resource.