You can find an example of integrating SWAT and MODFLOW here, http://swat.tamu.edu/software/swat-modflow/.

SWAT simulates surface runoff, soil water, and provides the boundary condition (deep percolation or groundwater recharge) for MODFLOW, and MODFLOW calculates groundwater flow and provides groundwater discharge to SWAT.

You may find details about the integration strategies in the link.

I hope this helps you.

Young

Sir on which type land we can use modflow, means If land is bed rock area so? can we use MODFLOW there?

Modflow can be used to model bedrock heterogeneity. You can review such studies on how modflow is used to represent as layers. Answer is yes, modflow can be used to represent unconsolidated as well as bedrock processes in varying layers.

thank you sir @timothy , Any limitation of area in km2? 

Pravin, there is no limit in area as SWAT works in large regions. Largest regions I used is 28,000 Km2 . Since the basic computation is hydrological units, SWAT and MODFLOW can simulate hydrology in smaller and larger scales. 

hello all

Is there any other wat to integrate SWAT and MODFLOW apart from SWAT_MODFLOW.exe and SWAT-MODFLOW Interface???In my case both the tools are not working.My watershed area is 1.21*10^5 km2.