Flows between ocean basins are often controlled by narrow channels and shallow sills. A multi-layer hydraulic control theory is developed for exchange flow through such constrictions. The theory is based on the inviscid shallow-water equations and extends the functional approach introduced by Gill (1977) and developed by Dalziel (1991). The flows considered are those in rectangular–cross-section channels connecting two large reservoirs, with a single constriction (sill and/or narrows). The exchange flow depends on the stratification in the two reservoirs, represented as a finite number of immiscible layers of (different) uniform density. For most cases the flow is ‘controlled’ at the constriction and often at other points along the channel (virtual controls) too. As with one- and two-layer hydraulics, controls are locations at which the flow passes from one solution branch to another, and at which (at least) one internal wave mode is stationary. The theory is applied to three-layer flows, which have two internal wave modes, predicting interface heights and layer fluxes from the given reservoir conditions. The theoretical results for three-layer flows are compared to a comprehensive set of laboratory experiments and found to give good agreement. The laboratory experiments also show other features of the flow, such as the formation of waves on the interfaces. The implications of the results for oceanographic flows and ocean modelling are discussed.