Table 1.

Ecological, geochemical and other environmental proxies used in palaeolimnology and how they can be used to understand the impacts of stressors on aquatic systems.

Sediment Proxy	Description of proxy	Variable (s) proxy used to reconstruct	Delta stressor variable can inform on	References
Diatoms	Cosmopolitan fossilised microscopic algae with silica cell walls (frustules). The different morphologies of diatoms make them easy to identify.	• Community compositional and abundance changes can be used to reconstruct changes in nutrient enrichment, salinity, pH and the thermal/light structure of lakes (e.g. through shifts in benthic to pelagic species) • Lake and hydrological evolution reconstructions using community compositional changes and stable isotopes from their silica cell walls (e.g. δ18O)	• Nutrient enrichment • Saline intrusion. • Natural to anthropogenic mediated hydrological alteration. • Industrial pollution • Natural to anthropogenic alterations to land-use • Natural to anthropogenic climate variability	Leng and Barker (2006), Duong et al. (2019), Briddon et al. (2020)
Algal pigments	The light absorbing compounds; chlorophylls and carotenoids of photosynthetic organisms	• Same as diatoms • Increased concentrations of cyanobacterial pigments could indicate the presence of cyanotoxins which are harmful to human and ecological health.	• Same as diatoms • Public health impacts of cyanotoxins through inferred abundance changes in cyanobacterial pigments.	Leavitt and Hodgson (2001), Waters et al. (2005)
Zooplankton remains: Chironomids and Cladocerans	The different morphologies of fossilised head capsules of non-biting midges (Chironomidae) and the chitinous remains of water fleas (Cladocera) which include the carapace, headshield, and appendages.	• Chironomid assemblage changes have been used to reconstruct air temperature (using chironomid-temperature transfer function), trophic status and water depth. • Cladocera are not always well-preserved but one of the only fossil representatives from the pelagic zone. Compositional and abundance changes are used to infer changes in pH, trophic status and water depth.	• Natural to anthropogenic climate change. • Natural to anthropogenic mediated hydrological alteration. • Nutrient enrichment	Brooks (2006); Wojewódka et al. (2020).
Ostracods	Fossilised calcium carbonate carapaces (shells) of the bi-valved crustacean which resemble water fleas. Ostracods are found in almost all aquatic habitats.	• Ratios of different geochemical elements and the stable isotope compositions of the ostracod shells can indicate changes to aquatic conditions • Presence/absence of species has been used to estimate past air temperature and salinity: The Mutual Ostracod Temperature Range (MOTR) and the Mutual Ostracod Salinity Range (MOSR).	• Saline intrusion. • Hydrological alterations • Temperature variability • Industrial pollution (heavy metals) • Oxygenation (changes to oxygen within a water body could be driven by hydrological change/lake ontogeny or development over time/anoxia events etc.)	Chivas et al. (1986), Gasse et al. (1987), Mischke et al. (2010)
Foraminifera (forams)	Single-celled protists whose shells are built of calcium carbonate (calcareous) or from tiny grains of sand stuck together (agglutinate)	Species compositional and shell geochemistry changes used to reconstruct changes in multiple environmental conditions such as salinity and dominant elemental composition.	• Saline intrusion • Natural to anthropogenic hydrological alterations • Land-use change • Nutrient enrichment	Scott and Medioli (1986), Benito et al. (2015)
Pollen	Microscopic fossilised male fertilising agents from plants, trees, grasses and weeds.	• Climate change using compositional changes • Environment changes through compositional and abundance changes (e.g. increase in pollen from agricultural crops indicate human land-use modification)	• Natural to anthropogenic climate variability • Natural to anthropogenic land-use change (e.g. conversion of mangrove forest to agriculture) • Natural to anthropogenic hydrological/water quality change	Bennett and Willis (2001), Hofmann (2002)
Plant macrofossils	Fossilised remains from vegetation that do not require microscopy to identify e.g. leaf, stem debris.	• Same as pollen	• Same as pollen	Birks (2001), Salgado et al. (2020)
Sediment grain size	The size of the grains within a sediment sample provides information on the composition, source, transportation and deposition of the sediment.	• Used to identify frequency and magnitude of flood events/the speed of water which determines the deposition of the sediment and the connectivity to the surrounding watershed.	• Flooding events • Natural to anthropogenic climate variability • Natural to anthropogenic alterations to watershed morphometry/hydrology	Tye and Coleman (1989), Liu et al. (2012), Chen et al. (2018)
Spheroidal carbonaceous particles (SCPs)	Distinct component of black carbon formed by the combustion of fossil fuels (coal and oil) at high temperatures (>1000°C).	Fossil fuel combustion	• Industrialisation • Urbanisation	Rose (2015), Engels et al. (2018)
Geochemical analysis: heavy metals and minerals.	Identifying the elemental composition of sediment using techniques including XRF (X-ray fluorescence)	• Concentrations and ratios of different elements can infer erosion and land-use change. • Increased concentrations of heavy metals can indicate industrial, sewerage and mining activity.	• Flooding events. • Natural to anthropogenic climate variability • Industrialisation (e.g. heavy metals) • Urbanisation • Mining activity	Last and Smol (2002), Vonk et al. (2015)
Stable isotopes from the sedimentary organic matter	Stable isotopes such as δ15N and δ13C can be used to determine the source of lake organic matter (e.g. terrestrial or allochthonous vs in-lake or autochthonous) and the trophic status of the lake. Measured using mass spectrometry.	• δ15N has been used to identify different N sources and processes of organic matter including sewerage and artificial fertiliser inputs, as well as N2-fixing cyanobacteria. • δ13C has been used to identify the productivity of lakes and inputs of terrestrial organic matter.	• Nutrient enrichment • Natural to human-mediated land-use change (e.g. conversion of mangrove forest to agriculture)	Meyers and Teranes (2001), Wengrat et al. (2018)
Sedimentation rates	Determined by measuring the radioactive nuclide signatures in the sediment such as 210Pb/137Cs etc.	• Changes to sedimentation rates can be used to reconstruct changes in sources of sediment and their transport. The deposition of sediments within a lake can also tell us about the thermal structure of the water column and its chemistry, its bathymetry and hydrological regime.	• Flooding events • Natural to human-mediated land-use change • Natural to anthropogenic climate variability • Natural to anthropogenic alterations to watershed morphometry/hydrology • Nutrient enrichment • Industrialisation • Urbanisation	Gell et al. (2009), Xu et al. (2017).