For an agricultural watershed, best management practice (BMP) is a conservational way to prevent non-point source pollution, soil and water loss and mitigate groundwater declination. In this dissertation, several BMPs of tail water recovery system, conservation tillage system and crop rotation were selected and evaluated in order to demonstrate the impacts of those activities on stream water quality and quantity. Besides, a land use change scenario was also evaluated. In order to evaluate the scenarios comprehensively, Soil and Water Assessment Tool (SWAT) and Annualized Agricultural Non-point Source Pollution (AnnAGNPS) were applied to simulate surface hydrology scenarios, and Modular flow (MODFLOW) models was used to simulate groundwater level change. This dissertation contains several novel methods regarding to model simulation including (i) using satellite imagery data to detect possible tail water recovery ponds, (ii) simulating surface and groundwater connected, (iii) selecting land use change area based on local trend and spatial relationship, (iv) comparing scenarios between two models. The outcomes from this dissertation included scenarios comparison on surface water quantity and quality, groundwater level change for long term simulation, and comparison between surface water models