Cleanest Lakes in Idaho: Top 25 Ranked by Water Quality
The single cleanest lake in Idaho is Nla 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 25 ranked list appears below.
Filtered to remove lakes with limited data (<3 sampling years). Sorted by overall water quality score.
The "cleanest" ranking on LakeGrade is composite: water clarity (Secchi), total phosphorus, and chlorophyll-a — the three core inputs to the LakeGrade rubric — taken together. The cleanest {{stateName}} lake on the current data is Nla Lake (A).
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 | Nla Lake | Gem | A | 17.6 ft | 19.7 µg/L | 1.3 µg/L | - |
| 2 | Nla Lake | Valley | A | 18.6 ft | 10.2 µg/L | 0.7 µg/L | - |
| 3 | Nla Lake | Blaine | A | 29.9 ft | 14.6 µg/L | 0.7 µg/L | - |
| 4 | Nla Lake | Kootenai | A | 19.2 ft | 16 µg/L | 2.1 µg/L | - |
| 5 | Nla Lake | Shoshone | A | — | 9.9 µg/L | 1.2 µg/L | - |
| 6 | Nla Lake | Valley | A | — | 18.2 µg/L | 3.9 µg/L | - |
| 7 | Nla Lake | Custer | A | — | 17.7 µg/L | 1 µg/L | - |
| 8 | Deadwood Reservoir | Valley | A | 17.2 ft | 14 µg/L | 1.7 µg/L | - |
| 9 | Ririe Reservoir | Bonneville | A | — | 19 µg/L | 3.2 µg/L | - |
| 10 | Bear Lake Off North Beach | Bear Lake | A | 21.7 ft | 11 µg/L | — | - |
| 11 | Bear Lake | Bear Lake | A | 19 ft | 4.2 µg/L | 0.3 µg/L | - |
| 12 | Bear Lake Se of St Charles Replicate of | Bear Lake | A | 19 ft | 4.5 µg/L | 0.3 µg/L | - |
| 13 | Usgs Lake | Kootenai | A | — | 4 µg/L | 1.6 µg/L | - |
| 14 | Ideq Lake | Kootenai | A | — | 5 µg/L | 1.3 µg/L | - |
| 15 | Ideq Lake | Kootenai | A | — | 4 µg/L | 1 µg/L | - |
| 16 | Ideq Lake | Kootenai | A | — | 3.5 µg/L | 1 µg/L | - |
| 17 | Cat Creek Lake | Elmore | A | — | 17 µg/L | 4.4 µg/L | - |
| 18 | Nla Lake | Bonner | A | 11 ft | 6.6 µg/L | 2.5 µg/L | - |
| 19 | Pasisades Reservoir | Bonneville | A | 10.5 ft | 15 µg/L | 2.9 µg/L | - |
| 20 | Palisades Reservoir | Bonneville | A | 12.5 ft | 18 µg/L | 1.9 µg/L | - |
| 21 | Deadwood Res Off Face of Dam Lake | Valley | A | — | 25 µg/L | 2.3 µg/L | - |
| 22 | Nla Lake | Bonner | B | 6.9 ft | 12 µg/L | 2 µg/L | - |
| 23 | Palisades Lake | Bonneville | B | 13.1 ft | 20.5 µg/L | 2.1 µg/L | - |
| 24 | Lake Lowell | Canyon | B | 7.2 ft | 17.5 µg/L | 1.5 µg/L | - |
| 25 | Arrowrock Reservoir | Elmore | B | 12.5 ft | 35 µg/L | 1.5 µg/L | - |
Clearest lakes in Idaho 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 Idaho is Nla Lake at 38.1 ft of Secchi visibility.
- 1. Nla Lake — 38.1 ft, Custer County
- 2. Nla Lake — 29.9 ft, Blaine County
- 3. Nla Lake — 23.3 ft, Boise County
- 4. Nla Lake — 22.1 ft, Shoshone County
- 5. Bear Lake Off North Beach — 21.7 ft, Bear Lake County
Frequently Asked Questions
What is the cleanest lake in Idaho?
Nla Lake has the highest water quality score in our 2026 Idaho 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 Idaho?
Among monitored Idaho lakes, Nla 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 Idaho has the cleanest water?
Idaho'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 Kootenai, Valley, and Bonneville produce the highest-scoring lakes.
What is the clearest lake in Idaho?
Nla Lake is the clearest lake in Idaho by water clarity, with a Secchi depth of 38.1 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 Idaho 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 Idaho 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 Idaho, 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 Idaho state norms and combined into a single 0–100 score. The lakes above are sorted by that combined score.Full methodology →
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Source: EPA National Aquatic Resource Surveys, 2026.