Coral Reef Diagnostics

Kenya

NOAA Coral Reef Watch

Regional summary of 21 dive sites. Figures are averages across the sites that report them (n = sites with a value); each site's own page has its individual values.

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05
Coral Reef Diagnostics
Photo: Anderson Mayfield/Coral Reef Diagnostics — Kenya - Brain Coral (Mombasa)
Country
Kenya
Sites
21
each linked below
Hard coral cover (regional mean)
30% ± 11% (std. dev.)
n = 20 of 21 sites. range 13–55%
Water temp. during surveys (regional mean)
32.0°C
n = 21 of 21 sites; surveyed Mar 2024–Apr 2024
Coral Health Index (regional mean)
1.50 / 5
n = 5 of 21 sites; 2.5 = average (below average — stressed)
Most recent water temperature record
16 Sep 2026 · Kenya
Most recent heat stress record
16 Sep 2026 · below alert level
Mean annual max degree heating weeks (DHW), last 5 years
2021–2025 · regional mean of 21 sites, 2 stations
Highest annual heat stress
in 2024 · Tanzania
Severe heat-stress years
1985–2025 · 3 in the last 10 years
Heat-stress figures: NOAA Coral Reef Watch — Kenya and Tanzania 5-km virtual stations. Each pill links its source record and carries the values behind it.
Regional summary

Kenya's shallow fringing reef flats, terraces, bommie fields, and restoration nurseries were surveyed in March-April 2024, during the Western Indian Ocean mass bleaching. Bleached tissue ranged from 45.4% to 95.4% of hard coral, and no coral growth form was reliably spared.

Heat stress

0481216Week of 2023-04-02: DHW 0.5°C-weeks (below the bleaching alert threshold); SST 29.77°CWeek of 2023-04-09: DHW 1.4°C-weeks (below the bleaching alert threshold); SST 29.85°CWeek of 2023-04-16: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 29.88°CWeek of 2023-04-23: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 29.28°CWeek of 2023-04-30: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 28.77°CWeek of 2023-05-07: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 28.46°CWeek of 2023-05-14: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 28.52°CWeek of 2023-05-21: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 28.60°CWeek of 2023-05-28: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 28.20°CWeek of 2023-06-04: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 27.90°CWeek of 2023-06-11: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 27.48°CWeek of 2023-06-18: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 27.19°CWeek of 2023-06-25: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 26.68°CWeek of 2023-07-02: DHW 1.6°C-weeks (below the bleaching alert threshold); SST 26.52°CWeek of 2023-07-09: DHW 0.7°C-weeks (below the bleaching alert threshold); SST 26.47°CWeek of 2024-02-25: DHW 1.2°C-weeks (below the bleaching alert threshold); SST 30.00°CWeek of 2024-03-03: DHW 3.1°C-weeks (below the bleaching alert threshold); SST 30.51°CWeek of 2024-03-10: DHW 5.1°C-weeks (Alert Level 1: significant bleaching likely); SST 30.69°CWeek of 2024-03-17: DHW 7.2°C-weeks (Alert Level 1: significant bleaching likely); SST 30.72°CWeek of 2024-03-24: DHW 9.2°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 30.77°CWeek of 2024-03-31: DHW 11.0°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 30.55°CWeek of 2024-04-07: DHW 12.6°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 30.42°CWeek of 2024-04-14: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 29.83°CWeek of 2024-04-21: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 29.38°CWeek of 2024-04-28: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 29.06°CWeek of 2024-05-05: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 28.54°CWeek of 2024-05-12: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 28.74°CWeek of 2024-05-19: DHW 13.5°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 28.44°CWeek of 2024-05-26: DHW 12.0°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 28.02°CWeek of 2024-06-02: DHW 10.1°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 28.10°CWeek of 2024-06-09: DHW 8.1°C-weeks (Alert Level 2+: severe bleaching and significant mortality likely); SST 27.88°CWeek of 2024-06-16: DHW 6.0°C-weeks (Alert Level 1: significant bleaching likely); SST 27.56°CWeek of 2024-06-23: DHW 4.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.28°CWeek of 2024-06-30: DHW 2.3°C-weeks (below the bleaching alert threshold); SST 26.95°CWeek of 2024-07-07: DHW 0.7°C-weeks (below the bleaching alert threshold); SST 26.94°CWeek of 2025-03-16: DHW 0.8°C-weeks (below the bleaching alert threshold); SST 29.69°CWeek of 2025-03-23: DHW 2.2°C-weeks (below the bleaching alert threshold); SST 30.10°CWeek of 2025-03-30: DHW 3.6°C-weeks (below the bleaching alert threshold); SST 30.08°CWeek of 2025-04-06: DHW 4.8°C-weeks (Alert Level 1: significant bleaching likely); SST 30.01°CWeek of 2025-04-13: DHW 6.0°C-weeks (Alert Level 1: significant bleaching likely); SST 30.00°CWeek of 2025-04-20: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 29.70°CWeek of 2025-04-27: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 29.59°CWeek of 2025-05-04: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 28.91°CWeek of 2025-05-11: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 28.13°CWeek of 2025-05-18: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 28.18°CWeek of 2025-05-25: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.98°CWeek of 2025-06-01: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.92°CWeek of 2025-06-08: DHW 6.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.70°CWeek of 2025-06-15: DHW 5.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.23°CWeek of 2025-06-22: DHW 3.7°C-weeks (below the bleaching alert threshold); SST 27.15°CWeek of 2025-06-29: DHW 2.4°C-weeks (below the bleaching alert threshold); SST 26.81°CWeek of 2025-07-06: DHW 1.2°C-weeks (below the bleaching alert threshold); SST 26.45°CWeek of 2026-03-01: DHW 0.1°C-weeks (below the bleaching alert threshold); SST 29.29°CWeek of 2026-03-08: DHW 0.1°C-weeks (below the bleaching alert threshold); SST 29.24°CWeek of 2026-03-15: DHW 0.1°C-weeks (below the bleaching alert threshold); SST 29.21°CWeek of 2026-03-22: DHW 0.1°C-weeks (below the bleaching alert threshold); SST 29.60°CWeek of 2026-03-29: DHW 1.3°C-weeks (below the bleaching alert threshold); SST 30.01°CWeek of 2026-04-05: DHW 2.6°C-weeks (below the bleaching alert threshold); SST 30.10°CWeek of 2026-04-12: DHW 3.8°C-weeks (below the bleaching alert threshold); SST 29.93°CWeek of 2026-04-19: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 29.61°CWeek of 2026-04-26: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 29.05°CWeek of 2026-05-03: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 29.03°CWeek of 2026-05-10: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 28.81°CWeek of 2026-05-17: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 28.50°CWeek of 2026-05-24: DHW 4.2°C-weeks (Alert Level 1: significant bleaching likely); SST 28.30°CWeek of 2026-05-31: DHW 4.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.77°CWeek of 2026-06-07: DHW 4.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.83°CWeek of 2026-06-14: DHW 4.1°C-weeks (Alert Level 1: significant bleaching likely); SST 27.58°CWeek of 2026-06-21: DHW 4.0°C-weeks (below the bleaching alert threshold); SST 27.11°CWeek of 2026-06-28: DHW 2.7°C-weeks (below the bleaching alert threshold); SST 26.72°CWeek of 2026-07-05: DHW 1.4°C-weeks (below the bleaching alert threshold); SST 26.61°CWeek of 2026-07-12: DHW 0.3°C-weeks (below the bleaching alert threshold); SST 26.43°C2426283032Bleaching threshold 29.8°C2023202420252026SST (°C)DHW (°C-weeks)
sea surface temperature (SST) (left axis)DHW under 2DHW 2–3DHW 3–5DHW 5–8DHW 8–10DHW over 10 (🔥 above 12)
Daily SST (line) and weekly maximum Degree Heating Weeks (bars), Jan 2023–Sep 2026, NOAA Coral Reef Watch 5-km Kenya virtual station. Dashed line: bleaching threshold (maximum monthly mean 28.8°C + 1°C). DHW ≥ 4: bleaching likely; ≥ 8: severe bleaching and mortality likely. A bar is drawn only where DHW exceeds zero, so a stretch with no bar is accumulated heat stress of zero, not missing data — the SST line runs the full period.

Long-term record: 4 years since 1985 reached 8 or more °C-weeks at NOAA’s Kenya, Tanzania stations. Download the annual DHW data (CSV).

21 sites in this region — click a marker to open that site.

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Regional setting

Kenya's reefs are mostly fringing reefs, the predominant type along mainland East Africa (Spalding et al. 2001). South of Malindi, a narrow coastal plain is backed by raised Pleistocene reef platforms standing above today's intertidal platform, and the continental shelf extends only about 5 km offshore; north of Malindi it widens to about 60 km. Fringing reefs are best developed in the south. Farther north, loose sediment and fresh water from the Athi-Galana-Sabaki and Tana rivers hold back reef growth, although fringing reefs occur around the Lamu islands and along a chain of about 50 calcareous barrier islands near Kiunga. Diversity also tends to be higher in the south, and Kenya's recorded coral fauna runs to about 55 genera and as many as 200 species. Before 1998, live coral typically covered about 30% of hard substrate, interspersed with seagrass and algal beds. In 1998, 50–90% of corals appeared to bleach and many died, and soft corals fared even worse. Kenya's first marine parks, at Malindi and Watamu, date from 1968, followed by Kisite and Mpunguti in 1978, Mombasa in 1986, and the Diani reserve in 1993, and protection has brought more fish, greater diversity, and higher live coral cover. Spalding et al. (2001) estimate about 630 km² of coral reef for Kenya, and Souter et al. (2021) put the whole Western Indian Ocean at about 15,180 km², nearly 6% of the world total.

Recovery in East Africa after 1998 was significant but patchy, and better on well-managed reefs, according to Wilkinson's (2006) summary of the 2004 status report. It named the growing coastal population, with land-based pollution and rising fishing pressure, as the largest threat, and listed Kenya with Tanzania and the Great Barrier Reef as the places with the highest recent densities of crown-of-thorns starfish. Souter et al. (2021) identify 1998 and 2016 as the two region-wide bleaching events in the Western Indian Ocean, with smaller episodes in 2005, 2007, and 2010 that interacted with fishing and local stressors. After the 2016 event, citizen-science surveys found that one site in five had lost more than half of its corals. Other published studies cited in that report point to 1998 mortality of 45–70%, after which cover never climbed back to its earlier level.

Overview

The 21 Kenya pins come from Anderson's survey of 11 March to 3 April 2024, during the Western Indian Ocean mass bleaching event. They run from Mombasa Marine Park south through Diani and the Shimoni-Wasini channel to Kisite-Mpunguti, and north through Kilifi and Watamu to Pate Island in the Lamu archipelago. All are shallow, from 0.5 m at Lower Mpunguti site 2 to 15 m at North Canyon: fringing reef flats, hardground terraces, bommie fields, and four restoration sites (the REEFolution nursery at Shimoni and three nurseries on Pate). The reef-building community changes along the coast. Foliose and laminar plates of Turbinaria, Montipora, and Echinopora type dominate at Sandy Patch and Diani, massive Porites bommies at the Mombasa Marine Park snorkel site, tabulate Acropora at Dolphin Point, and knobby Galaxea carpets cover Coral Garden and Kisite site 4.

Published hard coral cover at the 20 scored sites ranged from 12.8% at Chipopo, a restoration site, to 55.0% at Coral Garden in Kisite, which is wall-to-wall coral in clear blue water. The share of hard coral tissue bleached ranged from 45.4% at Sandy Patch and 46.6% at Brain Coral, both in Mombasa, to 95.3% at North Canyon and 95.4% at Ocean Trust Nursery. Six of the nine Kilifi, Watamu, and Pate sites exceeded 80%. Bofa carries the unit's only Coral Health Index, 2.25, just below the 2.5 average.

No single growth form was consistently spared. At Outer Kisite the branching Acropora thickets took the damage while massive Porites hillsides and plate terraces held pigment. At Bofa, Round Reef, and Uyombo the massive and brain corals were among the most completely bleached, and Turbinaria plates were the survivors at Bofa, Kilifi Bay, and Lower Mpunguti site 1. The Galaxea carpet held its color at Coral Garden but went white as a snowfield at Kisite site 4. Pink, mauve, violet, and chartreuse stress coloration recurred at Uyombo, North Canyon, and Kilifi Bay. Restoration stock was mixed, with pigmented and white fragments side by side on the same structures.

Crown-of-thorns predation was concentrated at Bofa, where at least nine individuals were found on already-bleached coral, with single or paired sightings at three other sites. Turtles, a trumpetfish aggregation, and a Spanish dancer on the Shimoni night dive stand out among the fauna.

Highlights

Notable observations (21)

Coral cover over time (pooled)

One point per year: the mean of every hard coral cover value available for this region that year — Anderson’s own dives and every independent survey station within 5 km of them. The vertical bar is the full range behind that mean. Different programs use different methods at different stations, so this is a regional summary, not a single comparable series. Years resting on fewer than three values are drawn as smaller points (1994, 1996, 2003, 2011, 2015, 2021). Marker shape: his own dives, other organizations’ surveys, a mix of both, that year.
0%17%34%51%68%1998 bleaching1994200920241994: mean 27% of 1 value1996: mean 26% of 2 values (range 24–27%)2003: mean 22% of 1 value2009: mean 21% of 5 values (range 9.7–42%)2010: mean 28% of 3 values (range 10–56%)2011: mean 25% of 2 values (range 25%)2013: mean 28% of 3 values (range 20–42%)2014: mean 18% of 7 values (range 13–25%)2015: mean 48% of 1 value2016: mean 29% of 13 values (range 15–52%)2017: mean 27% of 8 values (range 2.4–54%)2018: mean 38% of 10 values (range 8.0–53%)2019: mean 30% of 11 values (range 0.0–59%)2020: mean 24% of 3 values (range 18–29%)2021: mean 66% of 1 value2022: mean 27% of 4 values (range 8.8–56%)2023: mean 19% of 3 values (range 4.9–29%)2024: mean 29% of 23 values (range 13–55%)
Sites in this region (21)

% coral cover by method

Pooled across 8 dive sites

MethodMean % coral coverStd. dev. between dive sitesn dive sitesNote
Manual point count (author)25.1%±148frame-weighted 28.8% over 1,004 frames
manual_like_for_like22.6%±118frame-weighted 20.2% over 50 frames
CoralNet automated point classifier19.9%±178frame-weighted 19.2% over 50 frames; 8 of these dive sites are the SAME MEASUREMENT as the reference and are excluded from the ranking
CoralSCOP (SAM-based mask-sum), unedited photos26.4%±128frame-weighted 24.4% over 50 frames
Claude (Anthropic), blind point count20.4%±118frame-weighted 17.0% over 50 frames
In-house DINOv3 point classifier11.8%±6.38frame-weighted 11.0% over 50 frames

The mean is an UNWEIGHTED mean of the dive site values — each dive site counts once, whatever its photo count — which is the convention of the published tables and of every other figure on this page. The frame-weighted alternative is given per method in the Note column; where the two differ, the difference is a photo-count imbalance, not a coral-cover finding.

By dive site

Dive siteManual point countManual, same framesCoralNetCoralSCOP (unedited)ClaudeDINOv3
Coral Garden55.0%
n=178
45.0%
n=2
50.0%⚠
n=2
39.3%
n=2
40.0%
n=2
20.0%
n=2
Chipopo12.8%
n=40
26.7%
n=2
31.7%⚠
n=2
22.5%
n=2
30.0%
n=2
6.7%
n=2
Ocean Trust Nursery28.9%
n=62
26.7%
n=2
28.3%⚠
n=2
11.8%
n=2
26.7%
n=2
1.7%
n=2
Uyombo (UYQ quadrats)24.8%
n=375
21.7%
n=24
23.5%⚠
n=24
29.1%
n=24
17.5%
n=24
12.6%
n=24
Lower Mpunguti-site 118.1%
n=36
20.0%
n=1
0.0%⚠
n=1
16.8%
n=1
16.7%
n=1
13.3%
n=1
Round Reef (RRQ quadrats)17.8%
n=175
14.4%
n=16
8.8%⚠
n=16
15.7%
n=16
11.9%
n=16
8.3%
n=16
Pilot Nursery14.0%
n=21
13.3%
n=2
16.7%⚠
n=2
28.8%
n=2
10.0%
n=2
11.7%
n=2
Sandy Point29.3%
n=117
13.3%
n=1
0.0%⚠
n=1
47.2%
n=1
10.0%
n=1
20.0%
n=1

n under each value is the number of photographs that method scored at that dive site. ⚠ marks a cell that is not an independent check.

Reference: point-count on the photographs (a human scoring the same pixels the models see). Denominator: coral points / (30 − WATER − FISH); `Unk` is IN the denominator (Mayfield 2025 convention). Source: published verbatim (Mayfield 2025, Environments 12:276, Appendix A) ⚠ The published manual column and the four computer vision (CV) columns are on DIFFERENT FRAME SETS: the manual covers the site's full photo set (21–375 frames), the CV arms ran only on the 50-frame blind batch, which supplies 1–24 frames per site. The like-for-like row is the recomputed manual, not the published one. ⚠ The CV columns are on the OLD all-30 denominator while the published manual is on the settled rule; on these frames that understates cover by ~3.0 pp. The 50-frame batch is 6.3 pp poorer in cover than the survey average, so the CV columns are subset-distorted as well as denominator-shifted. Round Reef and Uyombo roll up 15 and 16 quadrat codes respectively.

Nearby external survey stations

82 independent survey records within 5 km of a site in this region (deduplicated across sites).

Show all 82 records

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

© Coral Reef Diagnostics.

References