Stone window sill - mortar/sealant missing

The Problem
Ugly effloresence stain under joint. This stain indicates that water was first absorbed by the masonry. It was drying from the visible surface and that it contained a significant amount of dissolved salts that were left behind when the water evaporated.

The Causes
Where did the water come from? It came from driving rain running down the window panes and along the sill. Water then leaks into the wall through the joint in the sill, wetting the masonry, including the mortar. Water, the universal solvent, dissolved various salts from the mortar and the masonry. During favourable weather conditions the wall dried out through the exterior surface, wicking interior moisture saturated with soluble salts from the mortar and some from the brick.

Long-term prognosis
The effloresence on the wall surface is but a symptom - of excessive amounts of water moving through the masonry. The mortar in the wall will eventually become weakened and can result in loss of structural integrity. It is more likely that the masonry will fail due to repeated freezing and thawing, if the wall is in a freezing climate like Canada and the northern U.S. Eventually the masonry will start to crumble in the areas adjacent to the surface effloresence; this is due to subfloresence, the drying of water from the interior masonry pores whereby the salts are deposited in the pores of the masonry and will eventually fill the pores and generate sufficient pressure to cause failure of the masonry.

Solution
What should have been done in the first place: place a metal flashing under the masonry sill, extending some 7 mm beyond the wall below it to act as a drip.