Coral Reef Diagnostics

Kenya - Pilot Nursery (Pate [Lamu]) snorkel

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05
Coral Reef Diagnostics
Photo: Anderson Mayfield/Coral Reef Diagnostics
Country
Survey date(s)
2024-04-03
Coordinates
-2.1660, 41.0390
Approximate position.
Coral cover
14%
Manual point count (21 photos) · other methods below
Coral bleached
94%
of hard coral tissue · Mayfield (2025), Environments 12:276
Observations
bleachingalgal overgrowth
Heat stress
Most recent heat load record
26 Oct 2026 · No heat stress
5-year thermal stress load
5-year mean max. degree heating weeks (DHW)
2021–2025
NOAA Coral Reef Watch — Kenya virtual station
i 5-year mean max. DHW is the mean of the annual maximum DHWs over the five complete years named above, not conditions today.
More infoKenya (NOAA CRW virtual station)
Photographs
33
20 shown on this page
Site summary
Read this summary in:

Pilot Nursery, off Pate Island, pairs empty rusting rebar restoration tables with stocked concrete beams carrying small outplanted Acropora and Pocillopora fragments — a genuine mix of pigmented and bleached nubbins rather than a uniform outcome. The natural reef here is continuous nodular Porites pavement rather than scattered heads, and it was found extensively bleached and heavily overrun by fleshy macroalgae, which grows up through the empty nursery tables. Published cover was 14% with 94% of coral tissue bleached; large schools of blackspotted sweetlips and a lionfish were recorded.

Water temp. during survey
32.0°C
(estimated from the TG7 underwater camera, not validated (Mayfield 2025, Environments 12:276, Table 1))

One other CRD dive site with its own page within 5 km shown in orange — click a marker to open its page.

6 of the 20 photographs on this page are shown beside the text that discusses them under "Site description" below.

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Photo credit & attribution

Site description

Setting

The full 33-frame set shows the setting — turbid green water, low-relief hardground, sand flats, and a standing canopy of red-brown fleshy macroalgae — and it also shows what is on the nursery structures and how much life is here.

General benthic features

Two kinds of restoration hardware are in the set, and they are in very different condition. The welded steel rebar tables are genuinely empty: five photographs all show open frames of rusting bar standing over bare sand with macroalgae growing up through them and no coral on them at all (e.g., Image 4).

The cast beams and blocks, though, are stocked. Five frames show twenty-plus outplanted nubbins cemented along the beams — small corymbose Acropora and nodular Pocillopora-type fragments, most of them a few centimeters across — together with pink crustose coralline patches, an orange encrusting sponge, and a heavy turf film on the concrete. The natural benthos is dominated by massive Porites: not scattered heads but continuous nodular Porites pavement (e.g., Image 1).

Two wide frames show a single knobby Porites carpet running out of frame in both directions, pale cream-green washed with lilac-mauve, with a handful of dark patches where tissue has already gone and algae has taken the skeleton. Cerioid faviids are present too — two frames show a cream, polygonal-corallite massive colony with red-brown weed already climbing over its flanks (e.g., Image 3).

In contrast, one frame shows a thumb-up beside a small cream-tan branching colony holding on in the algal canopy. Orange and yellow branching sponges stand on the algal-covered rock and are the brightest color seen — they are sponges, not coral. Macroalgae is the other headline. In two frames red-brown macroalgae are overgrowing massive colonies, climbing their flanks. One frame sums up the site: bare white skeleton and rubble between bushy stands of fleshy weed, with almost nothing intact in between (e.g., Image 2).

The same canopy stands well clear of the hardground in five frames, and it grows up through the empty steel tables, which is exactly the space outplants would need (e.g., Image 4).

Coral cover

Stressors

The condition of the outplanted fragments relative to the natural reef is the interesting part. The outplants are a mixed bag rather than a wipeout. One frame carries a fully brown-pigmented nodular colony on the upper beam alongside a bone-white branching fragment on the same face and a tan-gold branching nubbin on the lower beam. Another has two tan-gold Acropora-type fragments with polyps visibly extended sitting a hand's width from two chalk-white bleached nubbins. A third runs cream-tan nubbins up the beam leg with one stark white colony at the foot. So a real fraction of the outplanted stock still held pigment on 3 April. The natural massive corals around them did not. The outplants are nursery stock and must not be read as natural cover. One frame shows the same growth form at close range, colony after colony bleached to a uniform pale mauve-white with the nodules structurally intact and no algal overgrowth — bleached, not dead (e.g., Image 1). One frame is a bleached Porites ledge, chalk-white with a pink cast, overhanging a shaded gap. The lilac-pink tone recurs often enough across separate frames to read as pigmented bleaching rather than an artifact, but the frames are color-adjusted, so the exact hue should not be over-interpreted; the whiteness and the intact skeletal structure are what carry the call. Meandroid Platygyra brains are frequent and are the site's mortality signal: one frame is a large pale mauve-gray brain hemmed in by macroalgae, another shows Anderson's hand thumb-down over a pale Platygyra carrying a small tan corymbose Acropora on its crown, and a third is a meter-scale brain that Anderson recorded as dead. A solitary fungiid lies loose on the substrate in one frame, pale cream and, by Anderson's call, dead. There are no crown-of-thorns and no disease lesions anywhere in the 33 frames reviewed. Seawater here was an estimated 32.0°C during the survey (read from the TG7 underwater camera and not validated, per Mayfield 2025, Environments 12:276, Table 1; the Kenya survey-wide mean of 32.0°C matched the 1998 event), and NOAA recorded a peak of 13.5 degree-heating weeks on 18 April 2024, the highest for Kenya since records began in 1985. For the 2024 Kenya survey as a whole, Mayfield (2025, Environments 12:276) estimated that in situ temperatures ran about 1.3°C above NOAA's, so that "nearly 22 DHWs may actually have transpired"; those in situ readings came from the TG7 underwater camera and have not been validated.

Fish and other fauna

Blackspotted sweetlips (Plectorhinchus gaterinus) are here in large aggregations: three frames are dense schools of them over sand (e.g., Image 5), dozens are stacked under the bleached Porites ledge (e.g., Image 6), and singles and small groups appear in four more frames.

Surgeonfish and parrotfish cruise the open sand and the empty frames in three photographs; sergeant majors (Abudefduf) work the beams in two; a butterflyfish appears in two; small wrasses are on the rock throughout. A lionfish (Pterois) sits against the nursery structure — the only predator of note seen.

Comparisons with other data

Apart from our own published survey shown here, we found no other surveys at this site as of 2026. If you would like to share yours, please email us.

Dive record

Snorkel survey on 3 Apr 2024, 11:21-11:34, on the pilot restoration site off Pate Island, Lamu, in the middle of the 2024 Western Indian Ocean mass bleaching event. Surveys were run with PMCC / Northern Rangelands Trust.

CV model comparison

Computer-vision estimates from this site's own photographs are listed in the comparison table below, alongside the headline rather than merged into it.
Headline is the reference value; every other row is listed beside it for comparison and none is averaged in. ⚠ The methods did not all read the same photographs: the published manual value covers the site's 21 photographs; CoralNet and the in-house DINOv3 classifier ran on all 21 unedited photographs, Claude (blind) on all 21, and CoralSCOP on 16.
More infoOn the 21 frames Claude scored, with all 30 points in the denominator as in Claude's value, the manual count is 12%; that like-for-like figure, not the published value, is the fair comparison for Claude. ⚠ Claude's value counts all 30 points in the denominator, while the published manual value, CoralNet, and DINOv3 exclude water and fish points (the Mayfield 2025 convention), so Claude reads somewhat low on that basis alone. CoralSCOP (SAM-based mask-sum), edited photos: n/a — CoralSCOP was run only on the unedited Kenya photographs.
MethodHard coral cover (%)Photos (n) ± SE
Manual (published)14.0
CoralNet19.0n = 21
In-house DINOv332.6n = 21
CoralSCOP unedited11.2*n = 16
Claude14.1n = 21 · SE 4.6

The four computer-vision methods disagree by 21.4 pp (11.2–32.6%) and read on both sides of the manual point count (14.0%); the headline is the manual point count because a person's point count of the site's photographs is the reference the models are measured against.

*Based on only 16 reef-habitat photos; this estimate is less certain.

Data & links

All images from Coral Reef Diagnostics. Data are from Coral Reef Diagnostics.

© Coral Reef Diagnostics.