The majority of the municipality is situated in the lower valley of the Nemunas River, except for the Vilkyškiai Ridge [lt], which rises in the eastern part.

The southern border of the area is delineated by the Nemunas River, which leaves behind numerous old riverbeds, known as meanders, and receives several tributaries.

Along the banks of the Nemunas, the Rambynas hill is located.

The Pagėgiai municipality contains 5 seniūnijas (in English: elderships or wards);[2] the main town or village is listed for each.

Status: M, MST - city, town / K, GST - village / VS - farmstead