Land cover change from residential sprawl and urban expansion alter or disturb existing watershed dynamics. Transient land cover, such as forest clearings, ground preparation for construction of residential or commercial sites, or road expansions are reoccurring forms of disturbances in developing watersheds and change energy flow and ecosystem functions. We investigated the influence of transient land cover as a form of disturbance in watershed condition by measures of water quality, stream dynamics and stream fish assemblages. We utilized a geographic information system (GIS) and characterized the spatial distribution of land cover in 17 subwatersheds. Land cover type, their spatial extent and position, varied in influence on surface hydrology, water chemistry and stream geomorphology, and between low flow and pulse flow. Watersheds with forest as dominant land cover yielded lower concentrations for nitrate nitrogen, nitrite nitrogen and total phosphate and more stable streambed geomorphology compared to residential and urbanized catchments. Managed green areas and impervious surfaces exerted strongest influence on hydraulic pulse and water chemistry, with elevated total phosphate concentrations, by magnitudes greater suspended loads of settleable solids during pulse flow and electric conductivity during low flow conditions. Transient land cover differed in their influence on water quality based on spatial position within the catchment, water quality parameter measured, and flow condition. Their strongest effects on stream water parameter were found within 600 meter Euclidean distance upstream from sampling sites for turbidity measures during low flow, and within 90 meter Euclidean distance for electric conductivity and total phosphate concentrations during pulse flow. During low flow conditions transient land cover within a 90 meter wide riparian buffer for the entire stream network correlated strongest with stream condition. The importance of spatial position of transient land cover should be taken into consideration at initial stages of land use planning for developing watersheds.