Was Judea as desertified 2000 years ago as it is now?
There has always been a strong north-south rainfall gradient from approximately the Golan Heights (high rainfall), through Judaea and southwards into the arid Sinai desert. We know that this gradient once had a higher rainfall because there are abundant rainfall harvesting and groundwater collection structures, built by the Nabatean civilization about 400 BC to 100 AD. They are now long defunct because of climatic desiccation, but are characteristic of dry regions with marginal cultivation. Similar working structures can now be found in Oman, Iran and parts of north Africa. So it is reasonable to deduce that the region was once significantly wetter.

In addition to this overarching climatic gradient there is a very strong local rainfall gradient from the Israeli Highlands in the west, about 1100 mm, to the Dead Sea-Rift Valley in the east which receives about 100 mm per year. This is a rain shadow effect from the prevailing Mediterranean airflow to further east into the Arabian desert - obvious from the vegetation density on Google Earth. Masada currently receives about 200 mm per year, but it is very erratic, with huge inter-annual variability. One study of the Negev and adjacent dry areas concluded that the spotty distribution of annual rainfall doesn't average out - at least, not on any time-scale useful to humans. Because of its position in an intense rain-shadow, Masada will always have been dry.

There are two potential sources of water supply to places like Masada; springs, and ephemeral (very unreliable) flash floods. The springs are groundwater which has percolated through the limestone massif from the Israeli highlands around Jerusalem,. Hebron, etc. There are currently no springs in the immediate vicinity of Masada. There may once have been a spring under higher water-table conditions, but none that we know of historically. 

The solution used to supply Masada was to build two dams in canyons draining the Israeli highlands. Ephemeral flash floods were thereby intercepted and conveyed by gravity-drained aqueducts to tanks dug deep inside the Masada citadel. These tanks were of about 30 to 35 cubic metres capacity, so even allowing for evaporative and seepage losses in the aqueduct, the water supply could be topped up - provided the frequency of flash flood was sufficient. Even today it is likely that flash-floods would have been of adequate frequency. Under the slightly wetter regime of 2000 years ago, it is near certain that there would have been more than sufficient water every year. 

Unfortunately, there are no rainfall records from so far back, but some interesting general climatic inferences may be found in Issar A.S. (1990), 'Water Shall Flow from the Rock'.