Natural flow regime concepts and theories have established the justification for maintaining or restoring the range of natural hydrologic variability so that physiochemical processes, native biodiversity, and the evolutionary potential of aquatic and riparian assemblages can be sustained. A synthesis of recent research advances in hydroecology, coupled with stream classification using hydroecologically relevant indices, has produced the Hydroecological Integrity Assessment Process (HIP). HIP consists of (1) a regional classification of streams into hydrologic stream types based on flow data from long-term gaging-station records for relatively unmodified streams, (2) an identification of stream-type specific indices that address 11 subcomponents of the flow regime, (3) an ability to establish environmental flow standards, (4) an evaluation of hydrologic alteration, and (5) a capacity to conduct alternative analyses.