SHETRAN is designed primarily to model catchments, normally consisting of a catchment basin with a zero-flow boundary (the watershed, or catchment divide), and a channel network feeding surface and subsurface responses to precipitation to a single outflow reach of channel, although a full range of boundary conditions can be invoked to allow representation of, for example, small experimental plots.

Meteorological inputs to the catchment are: precipitation falling as rain or snow; measured or calculated potential evapotranspiration; and heat budgets used in calculating rates of snowmelt. Net precipitation to the ground surface is calculated from incoming precipitation and snowmelt, with allowance for interception, evaporation, and drainage from a vegetation canopy. Actual rates of evapotranspiration are calculated as a function of dynamic soil moisture conditions. Evaporation rates from leaf surfaces of the vegetation, from the soil surface, and from free water surfaces are calculated.

Infiltration into the ground surface occurs from either net precipitation or from surface water. Distribution of soil moisture content and tension in the unsaturated zone, and recharge to the saturated zone, are calculated. Saturated zone flows are calculated for a heterogeneous, anisotropic, unconfined aquifer. Exchange flows between the aquifer and a partly penetrating channel are computed, with or without a low permeability channel lining.

             Surface water is generated by either infiltration excess or saturation excess mechanisms, and is routed into the channel as sheet overland flow. Channel routing takes place through the channel network, through variable cross-section channel reaches, connected in any topology (distributaries as well as tributaries can be included, allowing looped networks). Backwater effects and overbank flooding can be modelled, at a level relevant to catchment modelling; i.e. SHETRAN is not a detailed hydraulic model of localized channel flow behaviour. Additional sources and sinks to the channel are from aquifer exchanges through the channel bed and banks, direct infiltration and evaporation at a dry channel bed, and direct extraction of channel water by plants.