Historical approaches to water quality control are finding new challenges as ecosystem issues are addressed in comprehensive water resources management programs. Important issues include the recognition that physical habitat conditions may be more important than water quality when ecosystem sustainability is the management objective. Although past emphasis has been on the control of continuous discharges, modern watershed management recognizes that achieving ecosystem sustainability requires control of runoff events that are variable in volume, timing, and frequency. This paper will explore how physical habitat management plays a dominant role in the determination of the ecosystem sustainability. Physical habitat is the result of an eco-hydro-geomorphic systems integration. This integration recognizes that magnitude, duration, and frequency, particularly in the hydrologic system contributes to an understanding of sensitivity and vulnerability in channel networks. Other topics of discussion include the critical linkages between contaminant concentration, duration of exposure, and frequency of recurrence in a watershed setting where differing levels of habitat stability are related to landscape use. The paper will also explore ecological engineering and associated ecohydrology and ecohydraulics in the development of modern watershed management.