GEOL30340 Low Temperature Geochemistry

Academic Year 2023/2024

This module focuses on low-temperature geochemistry and its use in understanding surface and near surface geological environments, focusing on surface waters and groundwaters. The emphasis is on the geochemical controls (e.g. Redox, pH) on the speciation, mobility and bioavailability of heavy metals and metalloids in surface waters, groundwaters, the oceans and near-surface sediments. Geochemical and biogeochemical reactions in early diagenetic processes is also introduced. The role of mineral surfaces and organic substrates in determining the migration behaviour of both metal and organic pollutants in groundwater systems is investigated. The geochemical principles that underpin the remediation of contaminated soils and groundwaters are dicussed. A number of whole-Earthgeochemical systems (carbon and nutrient cycles) are also introduced.

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Curricular information is subject to change

Learning Outcomes:

On completion of this module students should be able to:
Appreciate the range of controls that control the fate of metals and metalloids in surface- and ground-waters.
Predict the likely behaviour of a variety of metal/metalloid pollutants in a range of surface and shallow sub-surface environments, especially within groundwatersystems
Use simple computer codes to determine metal/metalloid speciation and be able to interpret the output.

Indicative Module Content:


Lecture 1: Introduction
Scope of the course. Review of terminology and concepts related to aqueous geochemistry. Examples of Earth’s low-temperature geochemical reservoirs. Concepts of water hardness, pH, alkalinity, salinity classification of waters. Sampling techniques and sample preservation. Acidification and filtration. Dissolved vs. suspended material. Revision of units. Some basic terminology for thermodynamics.

Lecture 2: Equilibrium thermodynamics with applications in geochemistry
Equilibrium thermodynamics revision. The equilibrium constant and solubility product. Gibbs free energy and calculation of equilibrium constants from thermodynamic data. Use of the van’t Hoff expression to calculate equilibrium constants at different temperatures. Concept of ionic strength, activity and activity coefficients. Debye-Huckel and other models for activity coefficient calculation. Measurement of disequilibrium and the ion activity product. The Saturation Index and the Saturation Ratio.

Lecture 3: Gecochemical reaction kinetics
Introduction to geochemical reaction kinetics. Activation energy. Effect of temperature on reaction kinetics. Reaction rates. Arrhenius equation. Controls on the rate of approach to equilibrium. Order of a reaction. Radioactive decay. Nucleation. Factors controlling the rate of dissolution and growth. Reaction, diffusion and mixed- control kinetics. Dissolution of silicates in water.

Lecture 4: Acid-Base reactions and the carbonate system
The dissolution and precipitation of calcite - role in deep-sea sediment diagenesis, karst formation, stream chemistry and the global CO2 cycle. Equilibrium/Dissociation constants in the carbonate system. Use of negative logarithms. Activities of different carbonate species as a function of pH. Importance of bicarbonate. Total and carbonate alkalinity. Alkalinity determination.

Lecture 5: Carbonate dissolution and karst waters
Calcium carbonate dissolution and the geochemistry of water in karst aquifers. Soil pCO2 and calcium carbonate solubility. Open and closed systems with respect to CO2. Undersaturation due to water mixing. Influence of high-Mg calcite and dolomite. Congruent and incongruent dissolution. Degassing and calcite precipitation. Examples from karst terrains and associated aquifers.

Lecture 6: Silicate weathering and soil formation
Silicate weathering reactions and soil formation. Soil chemistry. Field experimental/mass-balance methods to quantify chemical weathering in individual catchments. Dust deposition and aerosol contamination. Variations in chemical weathering as a function of lithology, climate, relief, water/rock contact time and vegetation. Nutrient loss to surface and groundwaters.

Lecture 7: Ion exchange processes
Clay minerals and cation exchange. Review of clay minerals and their ion-exchange characteristics. Cation exchange capacity (CEC) and its measurement. Selectivity and distribution coefficients. Adsorption in soils. Effect of pH on adsorption. Ion exchange characteristics of organic matter.

Lecture 8: Adsorption and desorption reactions
Adsorption effects. Inorganic colloids and colloid/particulate interactions. Linear and Langmuir isotherms. Surface complexation. Adsorption of metal cations. Anion adsorption. Desorption reactions. Examples of exchange reactions from the estuarine environment.

Lecture 9: Redox reactions
Oxidation and reduction reactions. The standard hydrogen electrode and Eh. Eh as a thermodynamic variable vs. a measurable quantity. Oxygen fugacity. Eh-pH diagrams. Role of photosynthesis, respiration and microbial decomposition in controlling oxygen in natural systems (esp. surface waters). Common redox reactions in nature involving nitrate, ferric iron and sulphate. Implications for water quality.

Lecture 10: Surface water quality
Surface water quality. Surface waters as a resource. Gas solubility and gas/water exchange. Biological oxygen demand. Chemical oxygen demand. Calculation of BOD curve downstream from effluent source. Surface layer re-aeration. Factors affecting water quality in rivers, lakes and reservoirs.

Lecture 11: Redox controls on metals in the environment
Eh-pH control on metal solubility and mobility. Co-precipitation and adsorption - role of oxyhydroxides. Case studies of Cu, Pb, Zn, Cd related to acid-mine drainage, tailings ponds and landfill sites. Aquifer and soil contamination. Acidification of surface waters.

Lecture 12: Heavy metals in the environment
Source of heavy metals - natural and anthropogenic. Speciation and complexation illustrated by U, Hg, Cu and Al. Formation of organometallic species and bioavailability of heavy metal contaminants.

Lecture 13: Ocean Chemistry 1
Speciation of metals in seawater. Chlorinity and salinity. Basic concepts of steady state conditions and residence time. Sr isotope curve. Redox conditions in the oceans. Chemical inputs and outputs. Redfield ratios.

Lecture 14: Ocean Chemistry 2
Ocean chemistry part 2. Nutrients in the oceans. Element fluxes to and from the ocean. Scavenging and recycling. Biological control on some elements. Conservative and non-conservative behaviour. Dissolved CO2 and acidification. The coastal and estuarine environment.

Lecture 15: Organic compounds in natural waters
CHONS & P. Organic compounds in natural waters. Definition of DOC and TOC. Major components of DOC. Humic substances. DOC in soil solutions, groundwater, rivers, lakes and oceans. Organic pollutants. Hydrophobicity and organic-water partition coefficients. Bioaccumulation. DDT case study. Polar and non-polar compounds and their adsorption characteristics. Biodegradation and bioremediation.

Lecture 16: Carbon geochemistry and carbon isotopes
The Geochemistry of carbon. Inorganic and organic carbon cycles. The ‘missing carbon sink’ and ocean acidification. Soil carbon and climate feedbacks. Carbon storage and sequestration in the subsurface. Mineral carbon sequestration. Use of carbon isotopes as tracers. Radiocarbon production. Radiocarbon dating.

Lecture 17: The bioeochemistry of nitrogen and sulphur
Nitrogen fixation, nitrification and denitrification. Nitrate as a pollutant. Use of nitrogen isotopes as tracers in environmental, food chain and palaeo-diet studies.Sulphur. The biogeochemistry of sulphur. H2S fluxes. Algae and DMS. Use of sulphur isotopes as tracers in the environment.

Lecture 18 The geochemistry of Phosphorus
Phosphorus minerals and their weathering rates. Eutrophication and algal blooms. The P cycle, global P reserves and sustainability. P recovery from municipal wastewaters.

Lecture 19: Waste disposal
Geochemical evolution of reactor landfills and other waste disposal sites. Geochemical aspects of nuclear waste disposal and storage. Geochemical aspects of CO2 storage in the subsurface and by mineral carbonation.

Lecture 20: Remediation of contaminated sites 1
Brownfield sites. Pump and treat methods and their limitations. Reactive barriers and other interceptor systems. Vapour extraction and air sparging methods. The problem of residual saturation. Monitored natural attenuation methods. Subsurface behaviour of organic pollutants.

Lecture 21: Remediation of contaminated sites 2
Methods to modify the redox conditions of the subsurface. Restauration of uranium-bearing aquifers. Monitored natural attenuation strategies (metals). Pinal Creek Basin case study. Potential unintended side effects of remedial actions.


Practical 1: Back to the basics
Review of the basics. Calculations involving the manipulation of units of concentration, pH calculation, valency and charge balance of selected species.

Practical 2: Mineral solubility calculations
Calculation of equilibrium constants for gypsum solubility from the basic thermodynamic data for enthalpies of formation. Recalculation of equilibrium constants using the Van’t Hoff equation.

Practical 3: Ionic strength, activity coefficients and activities
Calculation of the ionic strength of a solution from basic analytical data. Calculation of activity coefficients for selected species using the extended Debye Huckel equation. Calculation of activities for selected species. Calculation of saturation index with respect to calcite.

Practical 4: Atmospheric CO2 and surface water pH
Calculation of pH of water in equilibrium with the atmosphere assuming different levels of anthropogenic CO2. Investigation of the controls of ocean pH. Use of Bjerrum plots, equilibrium constants and activity coefficients. Summarise key finding of a research article.

Practical 5: Surface water quality, oxygen demand, oxygen sag curve calculation
Calculation of an oxygen sag curve as a function of time. Estimation of the time and distance downstream from a discharge point where dissolved oxygen reaches a minimum. Relate dissolved oxygen levels with the capacity of the river of supporting living organisms. Critically discuss sources and sinks of oxygen not considered in the Streeter and Phelps model.

Practical 6: Redox controls and heavy metal mobility
Prediction of metal mobility (divalent metal cations) as a function of pH and Eh conditions inferred from redox couples in estuarine (high organic content) and in open marine (low organic content) sediment pore waters.

Practical 7: Redox classification of modern sedimentary environments
Summarise key findings of a classic research article. Use dissolved oxygen to estimate redox conditions for bottom water samples from Chesapeake Bay (US). Interpret data on the basis of redox controls on Fe and Mn.

Practical 8: Geochemical reaction modelling
Introduction to and use of the WATEQ4F forward geochemical modelling program to carry out speciation, mineral dissolution and mineral precipitation calculations in waters as a function of temperature, pH and Eh.

Practical 9: Bemidji Case Study
Introduce the Bemidji contaminated site case study. Explain how the processes of contaminant plume degradation can be used to determine the presence of aerobic or anaerobic conditions. Estimate Eh values over time and use Eh-pH diagrams to estimate the likely behaviour of Fe-Mn hydroxides.

Student Effort Hours: 
Student Effort Type Hours




Specified Learning Activities


Autonomous Student Learning




Approaches to Teaching and Learning:
Practical activities (2 hours for nine weeks) are designed to reinforce and further develop concepts that are first introduced during the lectures. The first part of the course introduces the basic thermodynamics and geochemistry that is required. The second part of the course focuses on the application of these concepts to 'real world' problems (e.g. contaminated land, acid drainage, heavy metal mobility etc.). 
Requirements, Exclusions and Recommendations
Learning Requirements:

A good knowledge of inorganic chemistry is required for this module. Students should have taken Higher Level Leaving Certificate (or equivalent) chemistry. A First Year university or equivalent module in inorganic chemistry is highly desirable.

Module Requisites and Incompatibles
GEOL20100 - Environmental Geochemistry, GEOL30130 - Applied Geochemistry

Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade In Module Component Repeat Offered
Examination: End of trimester written exam 2 hour End of Trimester Exam No Standard conversion grade scale 40% No


Lab Report: Weekly write up of lab book Throughout the Trimester n/a Standard conversion grade scale 40% No


Multiple Choice Questionnaire: Mid-term MCQ Unspecified n/a Standard conversion grade scale 40% No



Carry forward of passed components
Resit In Terminal Exam
Autumn Yes - 2 Hour
Please see Student Jargon Buster for more information about remediation types and timing. 
Feedback Strategy/Strategies

• Feedback individually to students, post-assessment
• Group/class feedback, post-assessment

How will my Feedback be Delivered?

Weekly individual feedback to students by comments on work completed and recorded in laboratory notebooks each week. Individual and group feedback to students after mid-term MCQ exam.

Name Role
Dr Sam Kelley Lecturer / Co-Lecturer