Temporal changes in the water quality and ecology of an alluvial aquifer through an agricultural crop cycle

Irrigation is essential to intensive agriculture worldwide, particularly in semi-arid climates where rainfall is unreliable. The use of surface and groundwater for crop irrigation can alter aquifer dynamics by lowering water tables and degrading water quality through the leaching of agrochemicals, nutrients, and organic carbon. These changes pose significant risks to the integrity of groundwater ecosystems. To assess these impacts, we conducted a spatial and temporal study of groundwater chemistry and biota (using environmental DNA (eDNA)) in a shallow alluvial aquifer adjacent to an irrigated cotton farm in northern NSW, Australia. We sampled a series of wells in a transect stretching from an irrigated cotton farm toward the Namoi River, over an annual crop cycle. Groundwater levels declined over the year. Groundwater quality, particularly electrical conductivity and ammonia concentrations, varied with distance from the field. Water chemistry varied more between wells than over time, with wells close to the field showing distinctly different chemical characteristics to those further away. Drainage from the irrigated field was evident in the chemistry and isotopic signature of the groundwater, and also in biota. Taxa typical of surface waters and soils, and cotton DNA were more prominent in wells under the effect of irrigation. Biota displayed a potential 'ecological memory', where communities showed legacy effects related to past agricultural activities and hydraulic conditions. These results indicate the spatial extent of impacts of irrigation on shallow aquifers and confirm the direct and indirect effects of agricultural practices on groundwater levels, quality, and biotic communities within a short distance from an irrigated field. These findings have widespread relevance for the management of off-site impacts of irrigation activities.