Most radio-loud AGN are associated with jet-like structures that can extend over hundreds of kiloparsecs. These jets are a source of variable emission that covers most of the electromagnetic spectrum. The dominant component of the emission is produced through non-thermal processes like synchrotron radiation. In this study we investigate the contribution of hydrodynamic instabilities to the long term variability observed within these sources. This is done by undertaking 3D hydrodynamic simulations of a relativistic jet that is evolved with time. The simulation is constructed with the hydrodynamic code PLUTO and consists of a rectangular grid, spanning $256\times256\times512$ cells. The environment contains a uniform background medium into which less dense jet material is injected, at a Lorentz factor of 10. We have developed a post-processing code in order to determine the synchrotron emission that will be produced by this environment and calculate intensity maps at arbitrary viewing angles with respect to the hydrodynamic environment. In this code we assume that the emission is produced by non-thermal electrons in a power-law distribution and take into account geometric and relativistic effects. The resulting intensity maps show a similar large scale morphology to that of FR II type AGN, containing a central relativistic beam surrounded by lobe structures. The results also show the formation of time dependent structures, such as knots and blobs, due to hydrodynamic instabilities. It was found that these structures may cause a variation of up to $10\%$ in the total intensity.