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The San Francisquito Creek is swift, muddy and full of debris late Saturday morning, as seen from the bridge on the Menlo Park and Palo Alto border at Alma Street, looking toward El Camino Real and the rail bridge on Dec. 31, 2022. Photo by Andrea Gemmet.
Water flows down the San Francisquito Creek, which runs through Palo Alto and Menlo Park, after a storm in 2022. Photo by Andrea Gemmet.
Welcome to our tree column, “Ask your local arborist.” Each month, Peninsula arborist George Reno discusses a tree-related topic from general care and planting tips to how trees can impact your property. If you have a tree-related question or an idea for a topic to discuss, email lifestyle@embarcaderopublishing.com or post in the comments section at the end of this column.

December rains haven’t hit the area yet, but Palo Alto already saw a coastal flood advisory during the king tides at the start of the month. During flood advisories, many homeowners focus on roads, basements and power outages, but standing water can have serious consequences for your trees, as well.

Heavy clay soils throughout the Midpeninsula hold water longer than sandy soils, which means excess moisture can linger around tree roots long after floodwaters recede. Flooded roots can’t breathe properly, and that stress may weaken trees long before any visible symptoms appear.

This can be particularly problematic for low-lying neighborhoods that face elevated flood risk, especially near the bay and along creeks such as San Francisquito Creek, which runs through Palo Alto and Menlo Park. Large portions of the Peninsula fall within FEMA flood zones — Special Flood Hazard Areas, or SFHAs — including parts of San Mateo, Redwood City, Palo Alto and East Palo Alto.

Here’s what Peninsula homeowners should know when it comes to flooding and their trees:

Why flooding Is a problem for trees

Tree roots need oxygen. When soils become oversaturated, pore spaces that normally hold air fill with water instead. In landscapes with compacted or clay-heavy soils, water drains even more slowly. This means trees may sit in saturated soils longer than homeowners realize. Here’s what extended waterlogging can do to your trees:

  • Prevent roots from absorbing nutrients
  • Suffocate fine feeder roots that support overall tree health
  • Make trees more susceptible to pests and disease
  • Reduce root stability, increasing the risk of lean or uprooting
  • Trigger delayed decline weeks or months after the flood

Which trees are most vulnerable

While no tree enjoys prolonged flooding, certain species common to the region are especially sensitive:

  • Coast live oak
  • Valley oak
  • Deodar cedar
  • Some ornamental fruit trees
  • Mature conifers with shallow root systems

Meanwhile, trees adapted to seasonal wetlands or riparian corridors, such as willows or redwoods, tolerate flooding somewhat better. But even they can experience stress when water levels change too quickly.

What to expect after a flood

Symptoms of flood stress do not always show immediately. In fact, experts often warn that flooding can cause delayed decline, meaning you may notice issues weeks after the storm cycle ends. Keep an eye out for:

  • Yellowing leaves
  • Early leaf drop
  • Wilting despite wet soil
  • Reduced new growth in spring
  • Sudden leaning or soft soil around the root zone
  • Fungal growth at the base of the trunk

One important note: avoid adding fertilizer after flooding. When roots are stressed, they aren’t ready to take up nutrients, and added fertilizer can worsen decline.

How Peninsula soils worsen flooding impacts

Much of the greater Palo Alto area sits on a mix of heavy adobe clay and Bay mud, which drains poorly even in normal winter weather. During a coastal flood advisory, tides can push groundwater higher, reducing drainage even further. Water will most likely linger at the root zone long after surface flooding disappears.

In neighborhoods closer to the Bay, where soil is finer and salt exposure is more common, flooding can also introduce slight salinity. Some trees are sensitive to salt and may show leaf burn or thinning canopies later in the season.

While you cannot prevent the rain or tides, you can take these steps to reduce tree stress. 

Improve drainage where possible: Clear debris around root flares and ensure gutters and downspouts direct water away from trees.

Avoid compaction: Do not walk or drive on saturated soil. Compaction reduces oxygen levels even more.

Monitor standing water: If pooling persists for several days, make note of which areas drain poorly. A certified arborist can recommend long-term solutions such as grading adjustments or soil amendments.

Inspect your trees after the water recedes: Look for new leans, soil lifting, or cracking at the base. These can indicate loss of root anchorage.Schedule a post-storm assessment with a certified arborist: An expert can evaluate root health, check for structural instability, and recommend corrective pruning if needed. Early intervention often prevents larger problems later.


George Reno is a local arborist at The Davey Tree Expert Company in Menlo Park, which serves communities on the Peninsula, including Menlo Park, Atherton, Palo Alto and Redwood City. Reno can be reached at 866-923-5658.

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