1. Introduction
Sediment determines the physical environment of the ecological systems of rivers. The degree of water clarity, channel structure, and natural terrain can be altered by variations in the quantity and spatial distribution of different types of sediment. Extreme fluctuations in the physical and chemical characteristics disrupt the natural terrain and biological balance of aquatic biomes. The flow and upstream sediment supply have an impact on river sediment transportation, and changes in both variables affect the rate of sediment transport, as well as the locations where sediment is deposited or withdrawn [
1]. Comprehension of the processes of sedimentation and erosion pertaining to the diverse settings within a river is crucial for the management of sediment and sediment-associated habitats in rivers [
2]. Interrelated physical, chemical, and biological processes regulate sediment ecosystems and influence a sediment’s capacity to sustain a diverse, active, and well-functioning biological population [
3,
4]. Therefore, the quality of sediment has become a crucial factor in maintaining the health of benthic ecosystems and safeguarding aquatic biome environments. Sediment contamination is a debilitating issue for the scientific community because of the substantial amount of anthropogenic inputs that aquatic biomes are constantly receiving. The considerable amount of widespread pollutants stimulates changes in ecological equilibrium and degrades water and sediment quality [
2,
5]. The hydrological setting and morphology of rivers, wetlands, floodplains, estuaries, or coastal lagoons influence the accumulation of suspended particles and other related pollutants along water streams. Additionally, these pollutants have the ability to become a component of bottom sediment, which frequently propagates several miles downstream from chemical sources [
6,
7].
Among the common environmental contaminants that have a significant impact on human health, the environment, and ecosystems are hazardous metals and metalloids, which are released through a variety of anthropogenic and natural processes. The scale and production capacity of numerous industries, including the coal, building materials, metallurgy, and chemical industries, are rising swiftly in tandem with the rapid expansion of industrial economies in many countries [
8]. Like many developing countries worldwide, South Africa has experienced an immense increase in the demand for potable water resources due to a range of activities, including mining, urban stormwater, agricultural runoff, industrial discharges, and wastewater discharge, which are also the main contributors to aquatic biome and water resource contamination [
9]. South Africa is among the leading mineral-rich nations, ranking fifth globally in terms of the contribution of mining to gross development product [
10]. Despite their significance in achieving economic growth, prosperity, and progress on a national and international scale, mining and other sectors have demonstrated adverse environmental consequences [
9,
11]. For instance, the processes of gold (Au) mining has exposed the environmental waters to significant concentrations of radionuclides and other toxic elements [
12]. The ambient environmental surface and aquatic biomes may become increasingly contaminated with hazardous metals and metalloids such as arsenic (As), uranium (U), thorium (Th), lead (Pb), mercury (Hg), and cadmium (Cd) as a consequence of mining activities. The distribution of these hazardous elements is often diverse in riverbed sediment and water, and their amount transferred across the sediment–water interface depends on the physicochemical properties of the sediment and water [
13]. Moreover, their abundance in mining waste has the potential to constitute substantial amounts of sulphides, which enter aquatic environments through acid mine drainage and runoffs. As a result, sedimentation results in colloidal material that supplies the essential transportation and reservoirs for these pollutants [
14]. In aquatic reservoirs, As, Pb, Hg, Cd, U, and Th are non-biodegradable and may accumulate in sediments. Their toxicity, bioavailability, and solubility can vary based on their chemical form, with mobility being one of the key mechanisms causing elemental contamination that could be detrimental to human health and the biota [
14,
15].
Historical contamination still poses a significant threat to many aquatic biomes because contaminated sediment has been associated with impacts on both benthic and water column species [
2,
9]. Despite that, the underlying sediment may act as a reservoir to preserve the quality of the water by forming a long-lasting contaminant sink partitioned between pore water and sediment or suspended particulate [
16]. It could act as a contamination source under variable environmental conditions. For instance, numerous physicochemical processes, including sorption, oxidation-reduction, hydrolysis, temperature, salinity, and pH, may influence the chemistry of sediments. Consequently, the release of adsorbed contaminants in various chemical forms with high mobility and bioaccumulation rates increases the amount of toxic elements in both water and sediment. The water flow, size, and content of geological material can also have an impact on these processes [
1,
14,
17]. In addition, the constantly shifting relationship between metals in sediments and water flow is reflected in extreme hydrometeorology, whereas rising river flows as a result of climate change are causing silt from riverbeds to wash into the rivers’ upper reaches. As such, subterranean pollution deposits have the potential to gradually change the composition and quality of water [
13]. The prompt enrichment of hazardous metals and other pollutants in lake sediments is driven by both the effects of sediment adsorption and pollution source discharge, which pose a major threat to the aquatic ecosystem. For instance, As, Pb, Hg, Cd, U, and Th have exhibited acute and long-term toxicity to the benthic community, water column species, and human health, even at extremely low levels. Therefore, to assess the level of contamination and implement pollution control, it is essential to investigate hazardous element pollution in sediment and identify risk zones [
13,
18]. The scientific community has established systematic methods for the assessment and control of sediment quality as a result of the aquatic biome’s acquisition of toxic elements from various sources of contamination. Along with quantifying the concentration of trace elements, pollution indices are critical tools for the assessment of sediment quality and may have a major role in forecasting the sustainability of aquatic biomes in the future [
3,
8]. The aim of the study was to assess the sediment quality of the heavily contaminated perennial Juskei River in South Africa. Selected hazardous elements were quantified using inductively plasma coupled mass spectrometry for the determination of the degree of contamination through the assessment of pollution index parameters, such as contamination factor (CF), enrichment factor (EF), geo-accumulation index (Igeo), and pollution load index (PLI).