Managing diffuse pollution from agricultural land requires a spatially explicit risk assessment that can be applied over large areas. Major components of such assessments are the precise definition of both channel networks that often originate as small channels and streams, and Hydrologically Sensitive Areas (HSAs) of storm runoff that occur on land surfaces. Challenges relate to regions of complex topography and land use patterns, particularly those which have been heavily modified by arterial drainage. In this study, a national scale, transferrable workflow and analysis were developed using a specifically commissioned LiDAR survey. Research on the first half of Northern Ireland (6927 km2) is reported where field-edge drain to major river channels were mapped from 1 m (16 points per metre) digital terrain models, and in-field HSAs were defined across over 400,000 fields with a median field size of 0.86 ha. Manual drainage mapping supplemented with a novel automated drainage channel correction process resulted in an unparalleled high-resolution national drainage network with 37,320 km of channels, increasing mapped channel density from 0.9 km km−2 to 5.5 km km−2. The HSAs were based on a Soil Topographic Index (STI) system using hillslope and contributing area models combined with soil hydraulic characteristics. In all, 249 km2 of runoff risk HSAs were identified by extracting the top 95th percentile of the modelled STI as the areas with the highest propensity to generate in-field runoff. At field and individual farm scale these targeted risk maps of diffuse pollution were delivered to over 13,000 farmers and form part of the nationwide Soil Nutrient Health Scheme programme.