Cleanest Lakes in New York: Top 13 Ranked by Water Quality
The single cleanest lake in New York is Main Section 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 13 ranked list appears below.
Filtered to remove lakes with limited data (<3 sampling years). Sorted by overall water quality score.
Ranking the cleanest New York lakes means picking the basins that score high on all three water-quality dimensions, not just one. Main Section Lake leads the list with a grade of A, with Queneska Island 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 | Main Section Lake | Essex | A | 15.7 ft | 9.5 µg/L | 4.6 µg/L | - |
| 2 | Queneska Island Lake | Essex | A | 17.4 ft | 15 µg/L | 3.4 µg/L | - |
| 3 | Owasco Lake Platform | Cayuga | A | 11 ft | 6 µg/L | 2 µg/L | - |
| 4 | Seneca Lake Platform | Seneca | A | 11.5 ft | 6 µg/L | 2.6 µg/L | - |
| 5 | Isle la Motte Lake | Clinton | A | 15.4 ft | 8.7 µg/L | 5 µg/L | - |
| 6 | Isle la Motte Lake | Clinton | A | 12.5 ft | 12.3 µg/L | 4.6 µg/L | - |
| 7 | Main Section Lake | Clinton | A | 14.8 ft | 9.4 µg/L | 4.7 µg/L | - |
| 8 | Sodus Bay Lake | Wayne | B | 8 ft | 18 µg/L | 9.1 µg/L | - |
| 9 | Irondequoit Bay Lake | Monroe | C | 7 ft | 27.5 µg/L | 12.9 µg/L | - |
| 10 | Southern Section Lake | Essex | C | 2.6 ft | 22.9 µg/L | 10.4 µg/L | - |
| 11 | Southern Section Lake | Washington | D | 2 ft | 36.7 µg/L | 13.8 µg/L | - |
| 12 | Irondequoit Bay Lake | Monroe | D | 5.3 ft | — | 24.2 µg/L | - |
| 13 | Lk Ontario Lake | Monroe | D | — | 126 µg/L | 17.1 µg/L | - |
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?
Main Section Lake has the highest water quality score in our 2026 New York dataset (grade A), based on combined Secchi clarity, phosphorus, and chlorophyll-a measurements. Cleanliness here means low nutrient load, deep water clarity, and minimal algae — measured directly from EPA and state DNR samples.
What is the most polluted lake in New York?
Among monitored New York lakes, Lk Ontario 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 Essex, Clinton, and Monroe 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?
A and B grade lakes are typically safe for swimming under normal conditions. Chlorophyll-a below 10 µg/L means low risk of harmful algal blooms. Always check posted advisories before swimming — water quality changes seasonally, especially in late summer when blue-green algae bloom risk peaks.
How are these grades calculated?
Each lake is scored on three signals: Secchi depth (water clarity in feet), total phosphorus (nutrient load in µg/L), and chlorophyll-a (algae concentration in µg/L). Each gets a 0–100 sub-score relative to New York state norms. The three sub-scores average into the overall score, which maps to an A–F letter grade. Methodology details live on our methodology page.
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 lakes ranked above are the top 25 by our standardized 2026 grading.
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 →
Where to stay near New York's cleanest lakes
Compare cabins, resorts, and rentals near the clearest, lowest-algae lakes in New York — live availability and prices for your trip.
Top-rated places to stay near New York's cleanest lakes
Availability and prices from Stay22 partners (Booking.com, Vrbo, Expedia). We may earn a commission from bookings, at no extra cost to you.
Planning a trip to New York's cleanest lakes?
Get lake water-quality report cards plus the best cabin & lodging deals near New York's cleanest lakes — straight to your inbox. No spam, unsubscribe anytime.
Source: EPA National Aquatic Resource Surveys, 2026.