Alluvial streams re-shape their own geometry in response to changes imposed by nature or by humanity. Such adjustments may induce landscape and water surface elevations that are not compatible with the natural environment or existing activities. Therefore, for the purpose of planning, design and management, it is necessary to evaluate the variation of the levels, their effect on water and sediment movement and their general impacts to project developments. Both fieldwork and modelling techniques have been developed for assessing the hydrological impacts of such changes. In-stream sand quarry pits on alluvial rivers provide classic examples where streambed elevations are significantly affected by sedimentation changes, which occur concurrently with variation of water surface elevations. The hydrological impacts of a sand mining location on the River Kibos in Kenya are demonstrated by the aid of a simple improvised technique based on rating curve analysis, showing, for example, that due to sand mining the river bed and the corresponding low flow levels fell by about 0.8 m between 1977 and 1982. Noting the desire to make such assessments in advance so as to avoid the repair costs, a modelling procedure has been developed to enable a priori assessments. The dynamic equations describing the one-dimensional open-channel water and sediment flows, and the equation for the two-dimensional transient groundwater flow are solved simultaneously, and linked through a time-dependent interface boundary layer between the alluvial stream-aquifer systems. Considering the scarcity and uncertainty of data sets in this subject, the model has been applied to conceptual hydrologic systems to delineate interrelationships among individual hydrologic components as well as to determine the degree of influence of various parameters on the system behaviour Results by numerical experiments have suggested that baseflow recession curves for aggrading channels deviate steeply from the theoretical logarithmic recession curve as the river becomes more and more influent, while in a degrading reach the baseflow recession curves flatten, deviating from the theoretical recession curve as the river becomes more and more effluent. The hydrologic and fluvial impacts of in-stream sand borrow pit schemes have also been analysed. On the basis of some set-up options, the model allows for realistic predictions of changes to the water and sediment yields, and for the final selection of quarry schemes with least negative impact on the environment.