Agardite-(Y), with a refined formula of Cu2+ 5.70(Y0.69Ca0.31)[(As0.83P0.17)O4]3(OH)6·3H2O [ideally Cu2+ 6Y(AsO4)3(OH)6·3H2O, hexacopper(II) yttrium tris(arsenate) hexahydroxide trihydrate], belongs to the mixite mineral group which is characterized by the general formula Cu2+ 6 A(TO4)3(OH)6·3H2O, where nine-coordinated cations in the A-site include rare earth elements along with Al, Ca, Pb, or Bi, and the T-site contains P or As. This study presents the first structure determination of agardite-(Y). It is based on the single-crystal X-ray diffraction of a natural sample from Jote West mine, Pampa Larga Mining District, Copiapo, Chile. The general structural feature of agardite-(Y) is characterized by infinite chains of edge-sharing CuO5 square pyramids (site symmetry 1) extending down the c axis, connected in the ab plane by edge-sharing YO9 polyhedra (site symmetry -6..) and corner-sharing AsO4 tetrahedra (site symmetry m..). Hydroxyl groups occupy each corner of the CuO5-square pyramids not shared by a neighboring As or Y atom. Each YO9 polyhedron is surrounded by three tubular channels. The walls of the channels, parallel to the c axis, are six-membered hexagonal rings comprised of CuO5 and AsO4 polyhedra in a 2:1 ratio, and contain free molecules of lattice water.