The topography of Klaipėda County is divided into three regions, the highest in the east and lowest in the west: the Western Zemaičiai Plateau in the east, the Western Zemaičiai Plain in the center, and the Pajurys Lowland in the west and on the Baltic coast.

Klaipėda County borders Kaliningrad Oblast, Russia, to the south via the Nemunas, which drains into the Curonian Lagoon.

The Curonian Spit, a UNESCO World Heritage Site, is split between Klaipėda County, Lithuania and Kaliningrad Oblast, Russia.

The Lithuanian side of the spit is separated from mainland Lithuania via a small opening between Klaipėda and Smiltynė where the Curonian Lagoon drains into the Baltic Sea.

In locations throughout the county, annual precipitation rates can reach as high as 876 mm per year.