Deep drainage below the root zone is still the least understood component of the water balance, especially in cracking clay soils. It represents a waste of a valuable resource and can leach nitrogen out of the root zone. It has the potential to cause watertables to rise, with the accompanying risk of salinity. Drainage can move contaminants, such as salt and agrochemicals, into the groundwater.

The lysimeter facility at the Australian Cotton Research Institute, near Narrabri NSW, was used to study drainage, its contaminants and its interaction with groundwater in a heavy clay soil under a furrow-irrigated cotton – wheat rotation from 2006 to 2011.

Drainage during the cotton seasons varied from 0 – 74 mm, under wheat it was negligible and under fallow it was 23 mm. Drainage occurred in two forms: matrix drainage and by-pass drainage. The former occurs when the water storage capacity of the soil is filled due to prolonged rainy periods with any extra water becoming drainage. Drainage rates are not high (<0.5 mm/day) but can continue for periods of a month.

By-pass drainage occurs after furrow irrigation when water flows rapidly down macropores and by-passes the matrix of the subsoil. Peak drainage rates are reached 25 hours after irrigation and can reach more than 3 mm/day. The rate then declines exponentially over a week to about 0.5 mm/day. The amount of by-pass drainage appears to be controlled by the soil water deficit in the upper metre of soil. Drainage increases as the 0 – 0.5 m layer becomes drier, possibly due to greater cracking. However, larger deficits in the 0.5 – 1.0 m layer decrease drainage and appear important in mitigating by-pass drainage.

The risk of by-pass drainage is greatest when irrigation is necessary early in the cotton season, when the crop is too small to create a subsoil deficit between irrigations, especially if the subsoil was already wet before sowing.

The risk of matrix drainage can be minimized by managing both the rotation and irrigation scheduling to ensure there is sufficient deficit to accommodate likely inputs of water and irrigation at any time of year. Nevertheless there will always be times of above average rainfall when the profile is filled to capacity and drainage occurs.

However, some drainage is necessary to leach salts from the irrigation water that accumulate in the root zone. The electrical conductivity (EC) of matrix drainage is greater than by-pass drainage, suggesting matrix drainage is more efficient at leaching salt.

In addition to salt, drainage leaches nitrogen from the topsoil. During the 2008/09 cotton season approximately 9.5 kg N/ha – equivalent to 6% of that applied as fertilizer – was lost in drainage.

Seasonal drainage from the root zone appears to recharge the watertable at 16 m depth within weeks, although this result is still tentative. There is continuous downwards leakage of salty water from the upper, watertable aquifer into the lower confined aquifer, from which water is extracted for a variety of uses. This leakage is exacerbated by pumping from the lower aquifer.

The lysimeter was also used to test less expensive methods of estimating drainage. A barrel lysimeter installed near the lysimeter facility overestimated drainage, whereas the chloride mass balance method underestimated drainage.