Updated August 2026
Cleanest Lakes in New York: Top 8 Ranked by Water Quality
Ranked from the New York lakes that carry an A–F grade. Lakes with fewer than three sampling years, and lakes nobody has sampled, are not rated and are not ranked here.
The single cleanest lake in New York is Queneska Island Lake, with the highest combined water quality score in our 2026 dataset (grade A). Cleanliness is measured by Secchi depth (clarity), total phosphorus, and chlorophyll-a — all sourced from EPA Water Quality Portal and state agency sampling. The full top 8 ranked list appears below.
Ranking the cleanest New York lakes means picking the basins with the strongest nutrient-and-algae letters, then the clearer water among lakes that share a letter. Queneska Island Lake leads the list with a grade of A, with South Lake close behind.
The top of the cleanest-lakes list is dominated by deep, glacial, cold-water basins — the same basins that produce the A-grade bracket overall. The pattern is not coincidence: depth and watershed land-use are the dominant inputs to water-clarity and nutrient-loading both.
| Rank | Lake | County | Grade | Clarity | Phosphorus | Chlorophyll-a | Area |
|---|---|---|---|---|---|---|---|
| 1 | Queneska Island Lake | Essex | A | 17.4 ft | 15 µg/L | 3.4 µg/L | - |
| 2 | South Lake | Herkimer | A | — | 4 µg/L | 1.1 µg/L | 499 acres |
| 3 | West Pond | Herkimer | A | — | 10 µg/L | 3.3 µg/L | - |
| 4 | Squash Pond | Herkimer | A | — | 11 µg/L | 2 µg/L | - |
| 5 | Main Section Lake | Clinton | C | 14.8 ft | 12.1 µg/L | 4.7 µg/L | - |
| 6 | Little Clear Pond | Franklin | C | — | 16.5 µg/L | 5.2 µg/L | - |
| 7 | Hope Pond | Franklin | C | — | 10.5 µg/L | 7.6 µg/L | - |
| 8 | Southern Section Lake | Washington | D | 2 ft | 52.7 µg/L | 13.5 µg/L | - |
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New nutrient and algae samples can move a lake up or down this ranking. Unsubscribe anytime.
Clearest lakes in New York by water clarity
“Clearest” ranks by Secchi depth — how far you can see into the water — which can differ from the combined cleanliness score above. The clearest water in New York is Millsite Lake at 27.9 ft of Secchi visibility.
- 1. Millsite Lake — 27.9 ft, Jefferson County
- 2. Skaneateles Lake — 27.4 ft, Onondaga County
- 3. Lake George — 26.7 ft, Warren County
- 4. Oquaga Lake — 26.2 ft, Broome County
- 5. Indian Lake — 24.8 ft, Putnam County
Frequently Asked Questions
What is the cleanest lake in New York?
Queneska Island Lake has the highest water quality score in our 2026 New York dataset (grade A). Lakes are graded A to F on nutrients and algae — total phosphorus, total nitrogen, chlorophyll-a, and turbidity — measured against the EPA National Lakes Assessment 2022 condition classes for that lake's own ecoregion, so a lake is judged against the lakes it would naturally resemble. Cleanliness here means a low nutrient load and little algae, measured directly from EPA and state DNR samples; where two lakes tie on the letter, the deeper Secchi reading ranks first.
What is the most polluted lake in New York?
Among monitored New York lakes, Southern Section Lake ranks among the most polluted by combined phosphorus and chlorophyll-a load. See our full ranking on the most-polluted-lakes trend page for state-by-state details.
Where in New York has the cleanest water?
New York's clearest waters are concentrated in deeper, lower-nutrient glacial basins with forested or low-agriculture watersheds. Among the current top-ranked lakes above, counties like Herkimer, Franklin, and Essex produce the highest-scoring lakes.
What is the clearest lake in New York?
Millsite Lake is the clearest lake in New York by water clarity, with a Secchi depth of 27.9 feet — the deepest transparency in our 2026 dataset. "Clearest" ranks by Secchi depth (how far you can see into the water) specifically, while "cleanest" combines clarity with phosphorus and chlorophyll-a. See our full clearest-lakes ranking for New York for the top 25 by Secchi clarity.
Are these lakes safe to swim in?
Not on the letter alone. An A or B is a nutrients-and-algae classification, not a swimming clearance — it does not measure E. coli, cyanotoxins, or a posted beach closure, and a lake with low chlorophyll-a can still bloom. Always check current posted advisories before swimming: water quality changes seasonally, especially in late summer when blue-green algae bloom risk peaks.
How are these grades calculated?
The letter is nutrients and algae — phosphorus, nitrogen, chlorophyll-a, and turbidity — scored against EPA National Lakes Assessment 2022 condition classes for that lake’s ecoregion, not a New York-only 0–100 average and not an equal-weight mean with Secchi. Water clarity is shown; it is not scored. Lakes without enough recent sampling are UNRATED. Our methodology page has the full rubric.
What are the top 5 cleanest lakes in the US?
There is no single national ranking of cleanest lakes — each state agency uses different metrics. Crater Lake (Oregon) is widely cited as the clearest US lake, with Secchi depths over 30 m. Lake Tahoe and Lake Superior are also top-tier nationally. Within New York, the 8 lakes ranked above are the graded lakes with the highest letters in our 2026 dataset.
How we rank cleanest lakes
Cleanliness here means three things working together:
- Secchi clarity — how deep you can see into the water (in feet). Greater depth = clearer water = lower suspended sediment and algae.
- Total phosphorus — the nutrient that fuels algae. Lower phosphorus levels mean less algae growth potential.
- Chlorophyll-a — the green pigment in algae. Direct measurement of how much algae is currently in the water.
Each signal is normalized against New York state norms and combined into a single 0–100 score. The lakes above are sorted by that combined score.Full methodology →
More on clean water
The cleanest and dirtiest U.S. lakes in the monitoring record, ranked on EPA nutrient and algae condition classes across thousands of graded lakes.
How lakes are graded A–F on nutrients and algae using EPA ecoregion condition classes, what each letter means in the water, and why an A is not a clearance.
The cleanest U.S. lakes under 500 acres, ranked on measured nutrients, algae, and water clarity — with the size cutoff applied to the lake, not the sample.
A practical checklist for picking a lake with good water quality — clarity, phosphorus, algae history, depth, and the data to check before you commit.
Where to stay near New York's cleanest lakes
Compare cabins, resorts, and rentals around Queneska Island Lake and the other lakes in this ranking, with live availability and prices for your trip. Each pin on the map is one of the ranked lakes above.
Top-rated places to stay near Queneska Island Lake
Prices for Sep 11–13, 4 adults. Change dates on the map below.
Availability and prices from Stay22 partners (Booking.com, Vrbo, Expedia). We may earn a commission from bookings, at no extra cost to you.
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Source: EPA National Aquatic Resource Surveys, 2026.