There are many large lakes lining the park, reaching up to 90km² in surface area. Many are an intense turquoise colour as a result of rock flour particles left from glacial erosion, making the water look milky.
- Grey - A glacially-fed 32.6 km² lake
- Nordenskjöld - A 28m² lake pouring into Lake Pehoe through waterfall Salto Grande
- Pehoe - Fed by Paine river, running through waterfall Salto Grande
- Dickson - Fed by Dickson glacier and drained by Paine river
- Sarmiento - Surface area 90km², maximum depth 315m
- Del Toro - 202km² with a maximum depth of 300m (only a fraction of the lake is in the national park)