Clearest Lake in New York: Top 25 by Secchi Depth
The single clearest lake in New York is Millsite Lake in Jefferson County, with a Secchi depth of 27.9 feet — meaning a Secchi disk lowered from the surface disappears at that depth. Millsite Lake holds an overall water quality grade of A. The 25 clearest lakes in New York are ranked below by 2026 measurements.
Secchi depth is the standard scientific measure of lake water clarity. Greater depth means clearer water. Below, the 25 clearest lakes in New York from 2026 EPA + New York DNR sampling.
How clear are New York's clearest lakes?
Across the 158 New York lakes with Secchi clarity readings in our 2026 dataset, the 25 clearest range from 16.6 to 27.9 feet of visibility. Millsite Lake sits at the top, 0.5 ft clearer than the next lake on the list, well above the 20.3-foot median of this leading group — a spread that shows how quickly clarity falls off once you move past a state's handful of truly pristine waters.
The clearest water is not spread evenly. Madison County alone accounts for 6 of the 25 top-ranked lakes, with the rest drawn from 12 other counties. That clustering follows the terrain: deep, glacially carved basins ringed by forest take in little sediment or fertilizer runoff, so phosphorus stays low and the water stays transparent.
Clarity and overall health usually align here: 25 of these 25 lakes also earn an A- or B-range overall grade. Where the two diverge — a clear lake carrying a weaker grade — the cause is typically elevated phosphorus that transparency alone can't reveal, which is why our grade combines phosphorus and chlorophyll-a with Secchi depth rather than relying on clarity by itself.
| Rank | Lake | County | Secchi Depth | Grade | Max Depth | Area |
|---|---|---|---|---|---|---|
| 1 | Millsite Lake | Jefferson | 27.9 ft | A | - | - |
| 2 | Skaneateles Lake | Onondaga | 27.4 ft | A | - | - |
| 3 | Lake George | Warren | 26.7 ft | A | - | - |
| 4 | Oquaga Lake | Broome | 26.2 ft | A | - | 134 acres |
| 5 | Indian Lake | Putnam | 24.8 ft | A | - | - |
| 6 | Eagle Lake | Essex | 24.3 ft | A | - | - |
| 7 | Keuka Lake | Yates | 23.6 ft | A | - | - |
| 8 | Lake Placid | Essex | 23.1 ft | A | - | 2.2K acres |
| 9 | Mirror Lake | Essex | 22.6 ft | A | - | - |
| 10 | Blue Mtn Lake | Hamilton | 21 ft | A | - | - |
| 11 | Bradley Brook Reservoir | Madison | 20.7 ft | A | - | 141 acres |
| 12 | Tuscarora Lake | Madison | 20.5 ft | A | - | 362 acres |
| 13 | Lake Moraine | Madison | 20.3 ft | A | - | 260 acres |
| 14 | Lake Petonia | Chenango | 20.2 ft | A | - | - |
| 15 | Canadice Lake | Ontario | 18.8 ft | A | - | 657 acres |
| 16 | Anawanda Lake | Sullivan | 18.4 ft | A | - | 9 acres |
| 17 | Eaton Reservoir | Madison | 18.2 ft | A | - | - |
| 18 | Queechy Lake | Columbia | 18.1 ft | A | - | - |
| 19 | Lake Sunnyside | Warren | 17.8 ft | A | - | - |
| 20 | Canandaigua Lake | Ontario | 17.6 ft | A | - | - |
| 21 | Deruyter Reservoir | Madison | 17.6 ft | A | - | 560 acres |
| 22 | Queneska Island Lake | Essex | 17.4 ft | A | - | - |
| 23 | Lake Luzerne | Warren | 17.1 ft | A | - | 111 acres |
| 24 | Cazenovia Lake | Madison | 16.7 ft | A | - | - |
| 25 | Chenango Lake | Chenango | 16.6 ft | A | - | - |
Frequently Asked Questions
What is the clearest lake in New York?
Millsite Lake is the clearest lake in New York by Secchi depth, with water transparency of 27.9 feet. Secchi depth is measured by lowering a black-and-white disk until it disappears from view — deeper readings mean clearer water. Located in Jefferson County, Millsite Lake holds an overall water quality grade of A.
How is water clarity measured?
Water clarity is measured by Secchi depth, named after the 19th-century Italian astronomer Pietro Angelo Secchi who developed the method. A standardized black-and-white disk is lowered into the water on a rope; the depth (in feet or meters) at which the disk disappears from view is recorded. Greater Secchi depth means clearer water — usually a sign of low sediment, low phosphorus, and limited algae growth.
What makes a lake clear?
Lake clarity is driven by three factors: low suspended sediment (clay, silt), low nutrient load (especially phosphorus, which fuels algae), and low chlorophyll-a (active algae biomass). Deep glacial lakes with rocky basins and forested watersheds — common in northern New York — tend to be clearest because they have little soil runoff and limited nutrient input. Shallow agricultural-watershed lakes are typically less clear because they receive more sediment and fertilizer runoff.
Is the clearest lake the cleanest?
Not always. Clarity (Secchi depth) is one of three indicators we use; the others are total phosphorus and chlorophyll-a. A lake can be very clear but still have elevated phosphorus that just hasn't bloomed yet, or chlorophyll-a from a recent bloom that's still settling. The most reliable measure of overall lake health is the combined grade, which weights all three signals. See our companion [cleanest lakes in New York](/best/cleanest/ny) page for the combined-score ranking.
How does New York compare to other states?
New York's clearest waters compete with the deepest, most-pristine lakes in the Upper Midwest. Across Minnesota and Wisconsin combined, top-tier lakes typically register Secchi depths of 15–25 feet. Nationally, the gold standard is Crater Lake in Oregon (~30 m / ~100 ft) and Lake Tahoe (~20 m / ~65 ft). Within the Great Lakes region, New York's top lakes hold their own among the best.
Source: EPA National Aquatic Resource Surveys + state DNR Secchi sampling, 2026.