Lake Ohrid has 87.5 km of shoreline and covers an area of 358.2 km². Although the average depth of the lake is 164m, it has a maximum depth of 289m. The watershed of the lake includes steep mountains, as well as both Big and Small Prespa Lakes. The total area of the watershed is about 3,921 km². A little less than half of the water in the lake comes from its tributaries. On the Macedonian side, the Sateska and Koselska Rivers are the largest contributors. On the Albanian side, river flow is substantially less, but the Pogradec and Verdova Rivers are the largest contributors. The remaining inflow comes from the springs that flow into the couthern part of the lake, at St. Naum, Drilon and Tushemisht. These springs are fed by water flowing out of the porous karst mountains to the east, Galicica and Mali i Tharte. Over thousands of years, holes and channels have formed within the mountain rock. These channels carry water that originates in the Prespa watershed to Lake Ohrid. Because Lake Prespa sits about 150m above Lake Ohrid, its waters run downhill to Lake Ohrid through the channels in the karst. Water flows out of Lake Ohrid near Struga, into the Black Drim River. This river eventually runs all the way to Lake Skhodra and the Adriatic Sea.

Lake Ohrid is an ancient lake, formed by tectonic forces 2 to 3 million years ago, in the Terriary period. Because the lake is so old and is isolated by surrounding hills and mountains, a unique collection of plants and animals have evolved. These include a number of relict species, or "living fossils", and many endemic species, found only in the lake. For example, 10 of 17 identified fish species of the lake are endemic, as are many of the lake's snails, worms, and sponges. The lakeshore reed beds and wetlands provide critical habitat for hundreds of thousands of wintering water birds, including rare and threatened species such as the Dalmatian pelican, ferrugious duck, spotted eagle, and imperial eagle.