Jaime Ott, Orchard Advisor, UCCE Tehama, Shasta, Glenn, and Butte Counties
This winter is likely to be very wet, and now is the best time to start preparing. Wet winter weather can bring on a host of problems for orchards, including waterlogging, Phytophthora root and crown rot, and aerial Phytophthora infections. Flooding by rivers, standing water/soil saturation, and heavy rain events each come with their own risks and challenges. This article will summarize the major challenges growers might face in a wet year, introduce basic mitigation strategies, and point you to additional information.
Start preparing for wet weather: clear ditches, make sure drain tiles are working properly, dig trenches or build berms to redirect water away from your orchard.
Consider a phosphite/phosphonate foliar spray or chemigation this fall if your orchard has a history of flooding from nearby canals, creeks, or rivers.
Consider a phosphite/phosphonate foliar spray or chemigation, or a Ridomil Gold or Orondis chemigation next spring if you experienced prolonged flooding/standing water or if you see symptoms of Phytophthora root/crown rot.
Consider growing a cover crop or retaining resident vegetation to improve water infiltration, reduce erosion, and allow for earlier equipment access.
Keep records of any flooding or standing water.
Avoid pruning when there is rain in the 10-day forecast. Pruning right after harvest might be your best window this year.
Consider a phosphite/phosphonate foliar spray or chemigation, or a Ridomil Gold chemigation next spring if you see aerial Phytophthora infections of pruning wounds or young shoots.
*any mention of a pesticide product is for illustration only and is not an endorsement or a pesticide recommendation, simply the sharing of research results. Consult your PCA and always read the pesticide label; the label is law.
We are coming into what is predicted to be a very wet winter. Current predictions are that we will have normal rainfall in October and November, but very high rainfall amounts from December through February. Check out the 2026 September update on Dr. Daniel Swain’s Weather West YouTube channel for more information about the predictions for this year. In a wet, rainy winter, we may have to contend with flooding from nearby waterways, with standing water left over after flooding or from poor infiltration, or with saturated soil from high groundwater levels or from levee seeping. These conditions can lead to Phytophthora root/crown rot, waterlogging, or both.
Phytophthora root/crown rot is a disease caused by various Phytophthora species which take advantage of saturated soil to infect the roots and crown of the tree. If trees are exposed to flooding, this infection can start as high on the trunk as the floodwater reached, but generally these infections are seen coming up from the soil. Most Phytophthora species require at least 24 hours of soil saturation or flooding to initiate infection, so short-duration flooding or soil saturation is of less concern than prolonged periods of too much water. Symptoms are frequently not noticeable until after the tree breaks dormancy. Symptoms include yellowing leaves, poor vigor, lack of fine roots, amber-colored gumming associated with cankers (areas of dead tissue) on the trunk, and sudden tree collapse after bud push in the spring or after the weather warms up in early summer. If you excavate a tree, you may see a significant lack of fine roots, or distinct cankers with clearly defined edges on the larger roots.
Preventing saturated soil conditions or flooding in the first place is your first line of defense against Phytophthora root/crown rot (see more details below). However, if your orchard has historically flooded in wet years, you may consider applying a protective potassium phosphite or phosphonate (e.g. Kphite) foliar spray or chemigation this fall. This treatment can provide up to 5 months of protection against Phytophthora species. If you do experience prolonged periods of flooding, standing water, or soil saturation this winter, keep a close eye on your trees as they come out of dormancy—if you start to see symptoms of Phytophthora root/crown rot, consider applying a phosphite/phosphonate foliar spray, or a Ridomil Gold (mefenoxam) or Orondis (oxathiapiprolin) chemigation next spring. Any treatment needs to wait until the tree is truly out of dormancy, so plan to treat from mid-March through mid-May. Be especially watchful for symptoms in young trees (up to 3-4 years old), since they are more susceptible to infection and more likely to be killed if they become infected. In some cases, it could be justified to apply Orondis in the spring if a young block is flooded, before symptoms are visible. As a note, trees are much less susceptible to Phytophthora root/crown rot when they are dormant, so winter flooding is less concerning than flooding in the spring.
Waterlogging is a physiological problem which is not caused by an aggressive pathogen. When soil is saturated with water, there is little or no oxygen available and the roots (which require oxygen) suffocate. Generally, this takes some time (days to weeks) and is most damaging in cases with standing water, rather than moving water, and when the soil saturation happens while the trees are growing, rather than in the dormant season.
Like with Phytophthora root/crown rot, symptoms are frequently not noticeable until after the tree breaks dormancy. Symptoms include delayed budbreak, yellowing leaves, and poor vigor. Waterlogging generally leads to tree decline rather than a sudden collapse, but can result in tree death if the soil saturation is ongoing and severe. If you excavate a tree, you may see a significant lack of fine roots, and dead medium and larger roots. The duration of the soil saturation will affect the size of roots that are affected. Unlike with Phytophthora root/crown rot, you will not see a distinct boundary between dead and healthy tissue, and you will not see gumming on the trunk.
Preventing saturated soil conditions, standing water, or flooding is your only defense against waterlogging. Since this is a physiological problem, a lack of oxygen for the roots, the only way to improve conditions is to remove excess water from the soil. Waterlogging is worse on heavier soils, compacted soil, or soils with a hardpan layer. Practices which improve water movement through the soil or away from the orchard will help prevent or mitigate waterlogging.
General prevention for Phytophthora root/crown rot and waterlogging is, luckily, the same. In both cases, you want to prevent flooding, prevent standing water, and prevent soil saturation. After harvest is a good time to take stock for the upcoming winter: how can you keep water moving through and out of the root zone of your trees? Make sure your drainage ditches and culverts are clear and won’t back up into your orchard. Consider digging trenches to channel standing water away from your orchard. If your area is prone to flooding, consider building berms to protect your trees if nearby waterways overflow. Keep equipment out of the orchard when soil is wet, as compaction is much worse in wet soil.
This may be a good year to plant cover crops, or to allow the resident vegetation to grow in your orchard. Keeping the ground covered and roots in the soil will help with water infiltration, reduce runoff and erosion, and allow for earlier equipment access. The extra leaf area can also help dry out saturated soil more quickly. Check out this cover crop selector tool from the Western Cover Crop Council.
If you do experience flooding or standing water this winter, there are a few things to consider:
- Try to keep records of what happened: when did the flooding start? What areas were affected? How long was the area flooded? When did you notice the first symptoms?
- In most cases it is worth keeping the damaged trees for a while, both for insurance purposes and to see what recovers. This is especially true of cases where you are dealing primarily with waterlogging.
- Both waterlogging and Phytophthora root/crown rot compromise the root systems of your trees. When spring rolls around and you start thinking about irrigating, proceed with caution to not make your problems worse. Affected trees will take up less water than their healthy counterparts. They also might have a much shallower root system and need more frequent irrigations with a shorter duration. If you use the pressure chamber to guide your irrigation decisions, understand that the trees with compromised root systems might seem stressed, but in many cases adding more water won’t help the problem. Use a combination of pressure chamber and soil moisture monitoring to understand when it is time to irrigate affected trees.
- Prolonged flooding and soil saturation can have long-term impacts on your trees. It may take a year or two for trees to recover.
Aerial Phytophthora, or Phytophthora pruning wound canker, caused by Phytophthora syringae is another problem we could face if this winter is as wet as predicted. This is different from the Phytophthora infections mentioned above, when flood water causes infection high on the trunk of the tree, though some people will also refer to that as aerial Phytophthora. Aerial Phytophthora (Phytophthora pruning wound canker) made a comeback with the atmospheric rivers we had in 2023. Infection by Phytophthora syringae is favored in windy, rainy conditions. Symptoms include profuse gumming from cankers originating at pruning wounds or gumming at the base of dead young shoots. Cankers can expand rapidly in cool weather, sometimes leading to large branch dieback. In young trees, receiving large training cuts, this disease can be particularly damaging. Cankers stop expanding when the weather gets above 73ºF, and the pathogen dies out when the weather warms up in the summer.
Like with all pruning wound diseases, the risk of aerial Phytophthora can be minimized by pruning during dry weather. After harvest is an excellent time to make pruning cuts. Unprotected pruning wounds are susceptible for up to 4 weeks, but applying a phosphonate product directly to the fresh pruning wound reduces the chance of infection. Note that Phytophthora species are NOT true fungi, so fungicides like Topsin and Rhyme are not effective for preventing or treating Phytophthora infections.
If your orchard develops aerial Phytophthora, there are several chemical management tools at your disposal. Potassium phosphite or phosphonate can be applied as either a foliar spray or by chemigation. Ridomil Gold (mefenoxam) can be applied via chemigation. All these treatments need to be applied when the tree is fully out of dormancy and completely leafed out, coinciding with the spring root flush. This is generally mid-March through mid-May. Note that Orondis (oxathiapiprolin), which is very effective in treating Phytophthora root/crown rot, is not mobile enough to effectively treat aerial Phytophthora.
For more information check out these articles at sacvalleyorchards.com:
Waterlogged Orchards and Phytophthora
Wet winter concerns: Phytophthora and waterlogging
Wet years can lead to aerial Phytophthora outbreaks in almond orchards
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