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A field study investigated drainage and changes in soil water storage below the root-zone of annual crops on a sandy loam soil in the Victorian Mallee for 8 years. It was designed to compare the effects of the common long (18-month) fallow in a 3-year rotation (fallow-wheat-pea, FWP) with a rotation in which the fallow was replaced with mustard (Brassica juncea), viz. mustard-wheat-pea (MWP). Drainage was measured over 2 periods (1993-98 and 1998-2001) using 9 in situ drainage lysimeters in each rotation. The first period of similar to5 years was drier than average (mean annual rainfall 298 cf. 339 mm) and drainage was low and variable. Drainage was greater under the fallow rotation (average 0.24 mm/year) than under the non-fallow rotation (average <0.01 mm/year). The result for the fallow rotation did, however, include one lysimeter that recorded substantial drainage (10.6 mm over the 5 years). During the second period of measurement (&SIM;3 years), rainfall was above average (mean annual rainfall 356 cf. 339 mm) and drainage was greater. On average, drainage from the fallow rotation was 6.7 mm/year compared with the non-fallow rotation at 4.0 mm/year. There was again substantial variation between lysimeters. One lysimeter under MWP recorded 31.4 mm/year, and as in the earlier drier period, there were many lysimeters that recorded no drainage. During the drier first period (1993-98), changes in soil water storage between 1.5 and 5.5 m depth confirmed the tendency of the fallow rotation to increase deep drainage. Despite increases and decreases in subsoil water storage during the study, the cumulative change in water storage was positive and greatest under FWP (range 2.8-14.8 mm/year, av .9.6 mm/year) compared with MWP (range 5.3-9.8 mm/year, av. 7.4 mm/year) cropping sequences. Overall, the long fallow system has the potential to increase deep drainage by approximately 2 mm/year compared with a fully cropped system, over a wide annual rainfall range (134-438 mm). Further, this experiment reinforces the focus for the reduction of fallow practices for dryland salinity control in the Mallee region.