The East Alligator River is located 150 km east of Darwin and drains into van Dieman Gulf. Figure 1 shows the drainage basin which is composed of the World Heritage Listed Kakadu National Park, indigenous land forming part of Arnhem Land Aboriginal Reserve and two mining leases (Ranger and Jabiluka) currently held by Energy Resources of Australia (Figure 1). The mining leases are excised from Kakadu National Park [20] and are to be rehabilitated so that they are suitable for inclusion in Kakadu National Park. A former uranium mine, Nabarlek, is located on Cooper Creek in Arnhem Land [20]. Kakadu National Park is jointly managed by the traditional owners and the Australian Government through Parks Australia via a Board of Management.

The catchment area of the East Alligator River is about 7000 km² and the catchment area of Magela Creek is about 1600 km².

The main large-scale landforms of the East Alligator River catchment are an extensive sandstone upland known, as the Arnhem Land plateau, the spectacular edge of the plateau, known as the Arnhem escarpment, an extensive, highly weathered lowlands below the escarpment, known as the Koolpinyah surface, floodplains and wetlands, and deltaic estuarine floodplains along the lower river [21]. Each is briefly described below.

The Arnhem Land plateau is an exhumed, essentially sandstone, tabular upland and constitutes most of the catchment of the East Alligator River. It produces low sediment yields of predominantly sandy sediment [22]. A deeply incised, trellised drainage pattern has developed along closely spaced joints and faults in the sandstone [21]. It coincides with high terrain in Figure 1.

The Arnhem escarpment is a striking scenic feature at the edge of the sandstone plateau (edge of the high terrain in Figure 1). It varies from 30 to 330 m high and rivers exiting the plateau either flow over spectacular waterfalls (for e.g. Magela Falls on Magela Creek) or dissect the scarp by relatively long, narrow, deep bedrock gorges, which follow joints and faults (for e.g. East Alligator River).

The Koolpinyah surface is a monotonous lowland between the Arnhem escarpment and either erosion-resistant residuals or floodplains and wetlands or the deltaic estuarine floodplain (low terrain in Figure 1). It has developed across a wide range of lithologies and is a Tertiary lateritised palaeoplain [23,24] which experienced a second phase of lateritisation in the late Quaternary [25].

Rivers crossing the Koolpinyah Surface have cut shallow trenches which are occupied by sandy anabranching channels, floodplains, palaeochannels and wetlands [26- 28]. Magela Creek has been investigated in detail [27, 28]. Multiple Pleistocene terraces and palaeochannels flank the contemporary anabranching channel downstream of the Arnhem escarpment which started aggrading with sand about 5 - 7 ka [27]. This sand is slowly prograding downstream and is burying flood basins, billabongs and wetlands on lower Magela Creek [27]. Extensive flood basins of Holocene organic clay sediments lie between the upstream sandy alluvial plain and the downstream deltaic estuarine plain on the East Alligator River (Figure 1). The flood basin sediments stratigraphically overlie Holocene estuarine sediments [28].

The deltaic estuarine plain, based on results for the South Alligator River, exhibits four distinct channel types which in upstream sequence are the estuarine funnel, sinuous reach, cuspate meander reach and the upstream reach [29,30]. The deltaic estuarine plain developed in three major phases over the last 8 ka as sea level rose from about −14 m below sea level to its present level after 5.8 ka BP [29,30]. The “transgressive phase” (8 - 6.8 ka BP) marked the final marine flooding of the prior valley and the development of mangrove forests. Then the “big swamp phase” (6.8 - 5.3 ka BP) occurred as sea level stabilized around its present level and mangrove forests became established over most of the present estuarine floodplain. The “sinuous/cuspate phase” began about 5.3 ka BP and was characterized by the establishment of a meandering estuarine channel flanked by a marginal zone of mangroves. Freshwater swamps developed and overbank deposits were laid down on the floodplain surface. On Magela Creek, mangroves retreated downstream from Mudginberri after 4.4 ka BP and the strength of tidal connection was progressively severed and the former tidal channels were dismembered [28]. The channel and floodplain billabongs of [31,32] represent remnants of the former tidal channel. Between about 1.5 and 1.0 ka BP, freshwater wetlands formed over the lower 250 km² of Magela Creek (Figure 1) [28].

The Arnhem Land plateau and escarpment are composed of resistant, horizontally bedded, vertically jointed, strongly ferruginous, medium quartz sandstone of the Palaeoproterozoic (Statherian) Mamadawerre Sandstone, Gumarrimbang Sandstone, Marlgowa Sandstone and McKay Sandstone of the Kombolgie Subgroup [33,34]. The sandstone is generally more than 95% medium to coarse grained, moderately well sorted, subrounded to subangular quartz grains with minor lithic fragments of quartzite and quartz-feldspar granophyric intergrowths [33]. A series of volcanic members (Nungbalgarri Volcanics and Gilruth Volcanic Member) were extruded contemporaneously with the sandstone [33].

The Koolpinyah Surface developed largely on Late Archaean Nanambu Complex basement rocks and Proterozoic Lower Cahill Formation which is the host of uranium mineralization in this area [33].The carbonate rich rocks of the Cahill Formation were deformed and metamorphosed before deposition of the Kombolgie Subgroup [33].

The East Alligator River catchment is located in the summer rainfall-tropical climatic zone, characterized by heavy periodic rains and generally hot and humid conditions from November to March and essentially dry and mild to warm conditions from April to October [35]. Rainfall variability in the summer rainfall-tropical climatic zone is low to moderate but high daily totals are recorded during tropical cyclones [35]. On average, one cyclone per year affects the Northern Territory coast [36]. Mean and median annual rainfall are similar at each station (rainfall distribution is not skewed) [37] and decreases from about 1500 mm/year at the mouth of the East Alligator River to about 1000 mm/year in the south of the catchment. Alternating sub-decadal to multi-decadal, wet and dry periods have occurred over the last 136 years [37]. Consecutive time periods were usually statistically significantly different to each other and each wet and dry period were statistically identical to each other [37]. It is essential that any field measurements of geomorphic and hydrologic processes are correctly assigned to the relevant wet or dry period [37].

Figure 2 shows mean monthly discharge at gauging stations G8210010 on the East Alligator River and at G8210009 on Magela Creek (Figure 1). On the East Alligator River, streamflow usually commences in December and persists until April. During wet years, flow can persist right through the year although baseflow is very low. Streamflow on Magela Creek is similar to the East Alligator River, except that it never persists right through the year (Figure 2). The largest recorded flood at both stations occurred in late February/early March 2007.