In-Season and Long-Term Impacts of Flooding and Excessive Rain on Orchards

As snowpack melts, erosion along rivers and creeks threaten adjacent orchards.

The unusually wet 2023 winter and spring has had unprecedented impacts on our local orchard systems. However, the cumulative impacts of a barrage of atmospheric rivers and persistent standing water in some flooded areas may not be realized for another year. Cold and rainy conditions during bloom limited pollinator activity and impeded orchard access for spray operations, creating the ideal conditions for the onset of plant pests and disease issues. The timing of bud and shoot development has likely also been impacted as the buds for next year’s crop are formed during the current year; therefore, the wet and cold spring may also influence the development of the 2024 crop.

The bloom period for many Prunus species (almond, peach, cherry, plum, prune, etc.) was unusually protracted due to the high frequency of rain and cool temperatures. Saturated soil conditions limited orchard access, resulting in delayed shaking of mummy nuts in almond, an essential sanitation practice for management of navel orangeworm, a key insect pest With few bee flying hours available for pollination, and wet, cold conditions conducive to disease development (the crop outlook for 2023 remains uncertain.
Pistachio, walnut and pecan, all wind-pollinated crops, have experienced delayed bud break and shoot development. The progression of bud break appears to be at least 10 days behind the norm, and the timing and synchrony of male and female flower maturity is yet unknown.

Rains impeded orchard access, delaying the shaking of mummy nuts in almond orchards into early February 2023 (photo courtesy E. Fichtner.)

Orchards that have sustained flooding may be physiologically impacted by roots’ persistence in anoxic conditions and may also be exposed to waterborne plant pathogens. Over time, saturated soil will become depleted of oxygen by the roots and microbial communities, resulting in anoxic conditions that can lead to root mortality. The extent of damage to the roots may not be realized until the season progresses, and root damage may manifest with general canopy decline and anchorage issues. Many of the tree crops grown in California are grafted onto disease-resistant rootstocks. If flood water rises above the graft union, the benefit of these rootstocks is largely negated.

Flooding and excessive rain is conducive to plant diseases, including (from left) bacterial blast on almond (photo courtesy Florent Trouillas), Phytophthora [on pistachio] and brown rot [on peach] (photo courtesy Themis Michailides).
Many rootstocks have been selected over time for resistance to Phytophthora spp., a group of soilborne pathogens that create motile spores that swim at the water surface. These pathogens are common in surface water and incite canker diseases, particularly when the water level persists above the graft union. Symptoms of infection include general canopy decline and cankers, many of which ooze or ‘bleed’. The full suite of symptoms may not manifest until further into the growing season when the heat imposes stress on the trees.
The rainfall and flooding have additionally influenced the nutritional status of orchard soils. Cool, wet soil conditions slow the chemical and biological reactions that control the availability of nutrients for tree uptake. Micronutrients, present in only trace concentrations in soil, become particularly limited as the wet and cold create reductive conditions that promote lime-induced iron chlorosis, a common nutritional deficiency in prunes, almonds and citrus. In sites that have undergone whole orchard recycling with incorporation of woody biomass into the soil, saturated, anaerobic conditions may moderate the microbial activity needed to stimulate wood chip decomposition and further restrict nutrient availability until the soil warms.

Cool, moist soils may promote lime-induced iron chlorosis [on prune.]
As rivers breach their banks, rushing floodwater may transport the less-soluble nutrients, such as sulphate of potash (SOP) that is often applied in the autumn, away from the tree rootzone. As water moves through the soil profile, other nutrients such as nitrogen may be lost from the rootzone by leaching. The leaching will, however, ameliorate salt accumulation after years of drought, particularly in sites that have relied on saline groundwater for irrigation. Additionally, orchards adjacent to rivers and creeks are at risk of tree loss from erosion.

As the season progresses, growers should work closely with their PCAs, crop consultants and UCCE farm advisors to observe and document orchard changes in the 2023 season. Photographs should be taken of anomalies, such as delayed bud break, so comparisons may be made to past and future years. Additionally, photos of putative disease and insect issues may easily be shared with representatives from private industry as well as researchers in the UC system for both diagnosis and discussion of best management strategies. A suite of photos and management options for the most common pests and diseases of agricultural crops can be found at the UC IPM website (