Provided are nanoporous silicon nitride membranes and methods of making such membranes. The membranes can be part of a monolithic structure or free-standing. The membranes can be made by transfer of the nanoporous structure of a nanoporous silicon or silicon oxide film by, for example, reactive ion etching. The membranes can be used in, for example, filtration applications, hemodialysis applications, hemodialysis devices, laboratory separation devices, multi-well cell culture devices, electronic biosensors, optical biosensors, active pre-concentration filters for microfluidic devices.