The article describes the structural and functional analysis of the surface layer (S-layer) in the marine archaeon *Nitrosopumilus maritimus*, which plays a critical role in the nitrogen cycle by facilitating the uptake and channeling of ammonium ions. Using electron cryotomography and subtomogram averaging, researchers elucidated the structure of the S-layer, revealing its immunoglobulin-rich and glycan-decorated composition. Biochemical analyses confirmed the S-layer's ability to strongly bind ammonium, which is essential for the archaeon's ammonia oxidation. The S-layer is composed of repeating subunits of the NmSLP protein, arranged in a hexagonal pattern, and functions as a multichannel sieve, concentrating ammonium ions on the cell-facing side. Molecular simulations and cryo-EM studies further revealed that the S-layer's negatively charged residues facilitate cation binding and transport, enabling efficient ammonium enrichment. The S-layer's structure is conserved among many ammonia-oxidizing archaea, highlighting its importance in marine biogeochemical cycles. The study also identified glycans on the S-layer, which may contribute to cell protection and hydrophilicity. Overall, the S-layer acts as a critical molecular machine for ammonium binding and transport, essential for the survival and function of *N. maritimus* in marine environments.The article describes the structural and functional analysis of the surface layer (S-layer) in the marine archaeon *Nitrosopumilus maritimus*, which plays a critical role in the nitrogen cycle by facilitating the uptake and channeling of ammonium ions. Using electron cryotomography and subtomogram averaging, researchers elucidated the structure of the S-layer, revealing its immunoglobulin-rich and glycan-decorated composition. Biochemical analyses confirmed the S-layer's ability to strongly bind ammonium, which is essential for the archaeon's ammonia oxidation. The S-layer is composed of repeating subunits of the NmSLP protein, arranged in a hexagonal pattern, and functions as a multichannel sieve, concentrating ammonium ions on the cell-facing side. Molecular simulations and cryo-EM studies further revealed that the S-layer's negatively charged residues facilitate cation binding and transport, enabling efficient ammonium enrichment. The S-layer's structure is conserved among many ammonia-oxidizing archaea, highlighting its importance in marine biogeochemical cycles. The study also identified glycans on the S-layer, which may contribute to cell protection and hydrophilicity. Overall, the S-layer acts as a critical molecular machine for ammonium binding and transport, essential for the survival and function of *N. maritimus* in marine environments.