Pond shutdown is a strategy used to eliminate residual pathogens. For 2005–2011, we analysed the relationship between the prevalence of white spot disease (WSD) and the length of pond shutdown (LPS) and discussed its effectiveness for the prevention of WSD in Mexico. The LPS increased significantly from 2.1 months in 2005 to 3.1 months in 2011. The prevalence of WSD diminished significantly from 2005 to 2009, but no evidence of diminution was found when 2010 and 2011 were included in the time series. A χ2-test for trend indicated that the prevalence of WSD diminished significantly as LPS increased in 2005 through to 2009 and 2005 through to 2011 (P < 0.05). When analysed on an annual basis, the prevalence decreased significantly in relation with LPS in 2006 (P = 0.048), 2007 (P = 0.002), 2008 (P = 0.0001) and 2009 (P = 0.001); no evidence for decreasing the prevalence occurred in 2005 (P = 0.1), 2010 (P = 0.17) or 2011 (P = 0.52). The χ2-test adjusted for confounding indicated that decreases in prevalence in 2005 to 2009 could be attributed to increases of LPS rather than confounding variables such as increased resistance of shrimp, diminished virulence and improved cultivation practices. We discuss the possible relationship between the warm water temperatures in the Gulf of California and increases in the prevalence of WSD. We conclude that LPS has been an adequate management strategy for preventing WSD, supporting recent compulsory measures taken by the Mexican government to improve biosecurity in shrimp farms.