While governments and individuals strive to maintain the availability of high-quality water resources, many factors can “change the landscape” of water availability and quality, including drought, climate change, saltwater intrusion, aquifer depletion, population increases, and policy changes. Specialty crop producers, including nursery and greenhouse container operations, rely heavily on available high-quality water from surface and groundwater sources for crop production. Ideally, these growers should focus on increasing water application efficiency through proper construction and maintenance of irrigation systems, and timing of irrigation to minimize water and sediment runoff, which serve as the transport mechanism for agrichemical inputs and pathogens. Rainfall and irrigation runoff from specialty crop operations can contribute to impairment of groundwater and surface water resources both on-farm and into the surrounding environment. This review focuses on multiple facets of water use, reuse, and runoff in nursery and greenhouse production including current and future regulations, typical water contaminants in production runoff and available remediation technologies, and minimizing water loss and runoff (both on-site and off-site). Water filtration and treatment for the removal of sediment, pathogens, and agrichemicals are discussed, highlighting not only existing understanding but also knowledge gaps. Container-grown crop producers can either adopt research-based best management practices proactively to minimize the economic and environmental risk of limited access to high-quality water, be required to change by external factors such as regulations and fines, or adapt production practices over time as a result of changing climate conditions.