A systems approach was applied to four horticultural nurseries in Oregon to inform <i>Phytophthora</i> disease management. First, a hazard analysis was conducted to determine sources of <i>Phytophthora</i> contamination in the nursery production cycle. Plants, potting media, used containers, water, greenhouse soil, and container yard substrates were systematically sampled from the propagation phase to the field production phase. Overall, a total of 674 <i>Phytophthora</i> isolates representing 28 different species or taxa were identified. Each taxon was then categorized according to ecological guild to better assess disease risk. Approximately 29% of the <i>Phytophthora </i>isolates were recovered from untreated water reservoirs but most of the waterborne taxa were considered aquatic opportunists rather than plant pathogens. However, three novel taxa with unknown pathogenicity, including two hybrids, were detected from untreated water. Only 1% of the isolates were recovered from potting media, 2% from used containers, and 0.6% from treated irrigation water. More than 16% of the isolates were recovered from soil and gravel substrates in greenhouses, container yards, and in-ground field production sites, and many of these soil isolates belonged to plant pathogenic taxa that were also recovered from plants (51% of isolates). These findings identify contamination hazards and target critical control points for management of <i>Phytophthora</i> diseases in horticultural nurseries.