The interaction of siphon ow with an initially linear Alfven wave within an isolated chromospheric loop is investigated. The loop is modelled using 1.5D magnetohydrodynamics (MHD). The siphon flow undergoes a hydrodynamic (HD) shock, which allows the Alfven instability to amplify the propagating waves as they interact with the shock and loop footpoints. The amplification leads to non-linear processes strongly altering the loop equilibrium. Azimuthal twists of 50 km/s are generated and the loop becomes globally twisted with an azimuthal magnetic field 5 times stronger than the longitudinal field. The flow is accelerated to 70 km/s due to the propagating shock waves that form. Near the end of the simulation, where the non-linear processes are strongest, flow reversal is seen within the descending leg of the loop, generating up flows up to 28 km/s. This flow reversal leads to photospheric material being `pulled' into the loop and spreading along its entirety. Within about 2.5 h the density increases by a factor of about 30 its original value.