Irrigation water may harbor Phytophthora capsici, and irrigating susceptible vegetable crops with infested water can initiate epidemics. In this study, we evaluated the genetic structure of 106 P. capsici isolates collected from a creek used for irrigation (2002, 2003, and 2006) and from a field adjacent to the creek (2001) using six polymorphic nuclear loci. Bayesian clustering analysis detected four clusters in the sample, and some clusters occurred more or less frequently in certain years. In 2006, isolates belonging to cluster four predominated in the sampling. Mean pairwise FST values (0.008 to 0.065) indicated low differentiation between categories, but the most differentiation was observed when 2006 was compared to 2001 and 2002. Differences in isolate phenotypic traits were observed year-to-year. Isolates insensitive to mefenoxam were more common in 2006 and 2003 than in 2002 and 2001. The mating type ratio was approximately 1:1 in 2002 and 2003, but was skewed toward A1 in 2001 and toward A2 in 2006. Since irrigation water can remain infested or become reinfested annually with P. capsici for years after the adjacent fields are transitioned to nonsusceptible crops, growers are advised to avoid potentially infested irrigation water even after rotating to nonhost crops for several years.