Soil and Water Pollution, Concepts and Theory

Course content

Review of the biogeochemistry of soils and natural waters critical for pollutant fate and effects. Environmental microbiology: microbial community theory, terrestrial and aquatic microbial lifestyles emphasizing microbial degrader populations. Reviews of concepts used for characterization of abiotic and microbial status of soils and natural waters.

Overview of priority pollutants such as heavy metals, radionuclides, pesticides, medicine, hormones,  solvents, detergents, antibiotic-resistant genes, and microbial pathogens in soil and aqueous environments, with emphasis on their sources, physical-chemical, and microbiological properties. The main part of the course focus on application of chemical and microbial principles to study and quantify pollutant bioavailability and fate. This includes solubility, and speciation of toxic inorganic solutes, and pollutant binding via ion exchange, surface complexation, and partitioning into organic matter and living media (bioconcentration, biomagnification). The role of particle surfaces for pollutant transformations. Hydrolysis and photochemical degradation of organic pollutants. Redox processes, zonations and sequences. Microbial/enzymatic degradation and mineralization pathways, metabolite formation, and transformation kinetics. Software for estimation of organic pollutant properties, and for computing speciation and binding (MINTEQ). Theory is supported by real-life examples.

Biodegradation and toxicity, microbe-metal interactions, metal toxicity and resistance; xenogenetic pollutants and antibiotic resistance.

Outlook: Emerging pollutants, genes and microorganisms


MSc Programme in Environmental Science
MSc Programme in Nature Management
MSc Programme in Agriculture

MSc Programme in Chemistry

Learning outcome

The objectives of the course are to comprehend and to study how: i) soils and natural waters are affected by pollution, ii) soils function as “filters” for natural attenuation of pollutants, iii) pollutants bind and transform, and iv) how we quantify the chemical and microbial processes.

After completion you should be able to:


  • Classify and provide overview of main pollutants in terrestrial ecosystems, and to present knowledge on the relationships between land use, soil and water quality
  • Describe how microbes interact with soils and how this affect pollutant degradation
  • Describe key properties and processes of pollutants critical for sorption, abiotic and microbial degradation, bioavailability and biomagnification in terrestrial systems
  • Classify and summarize the molecular mechanisms controlling pollutant degradation, transformation and bonding in soils and water
  • Acquire knowledge on the methods available for predicting the fate of chemical substances in soil and aquatic environments
  • Describe analytical procedures and monitoring strategies for pollutants in terrestrial systems



  • Retrieve and critical examine environmental chemical data
  • Apply and demonstrate the use of general principles from chemistry and microbiology for quantification and evaluation of pollutant fate and balances
  • Estimate chemical and physical properties of pollutants and pollutant fate in terrestrial ecosystems
  • Suggest methods and approaches used for assessing microbe-pollutant interactions
  • Critically report on pollutant fate and remediation in terrestrial and aquatic environments



  • Combine data and information from different sources in calculus, prediction and evaluation of pollutant mass balances, fate and effects in soils and aquatic systems
  • Judge the relative importance of various sorption and transformation processes on the overall distribution and fate of chemical substances in soil and aquatic environments
  • Diagnose the processes critical for the fate of any pollutant, and critical select tools for analysis and evaluation
  • Discuss and assess the complexity of how land use affect soil and water quality
  • Collaborate with fellow students on problem solving and reporting critical pollutant assessments
  • Point to new directions and aspects of emerging pollutants

Lectures, theoretical exercises incl. use of computer computations, and project work. One half-day excursion comprising examples of soil and water pollution, remediation, and monitoring. Lectures to provide overview and highlight main topics. Emphasis on computational exercises to train the chemical and microbial principles and models taught. Computer exercises comprise QSAR computation of pollutant properties, and equilibrium speciation. Project work focus on description, quantification and discusion of contemporary cases of water and soil pollution and the remediation technologies which can be used. The projects draw on the general insight in chemical, and microbial processes presented in the course. Each project is solved by groups (3 – 5) of students and it is presented as a written report which is presented orally to the class.

The full curriculum can be found at Absalon

Hansen, H.C.B. (ed)(2015) Soil Pollution: Biogeochemistry and Modelling - including theoretical exercises.

Schwarzenbach, R.P. et al. (2005) Environmental Organic Chemistry, 2nd Ed., Wiley, different chapters

Maier, R.M. et al. (2014) Environmental Microbiology, 3rd Ed., Ch. 1-3 (brush-up reading), 4, 6, 15-20 and 31. Also to be used (other chapters) on follow-up course in Block 2.

Handout notes and few journal papers.

Software for speciation analysis (MINTEQ)

Software for QSAR estimation of pollutant properties (EPISUITE)

Excursion material

The course builds on basic chemical principles corresponding to the level of 1st year university chemistry. Physical chemistry is applied for solving problems in environmental chemistry and hence basic understanding of thermodynamics and kinetics is an advantage. Similarly, the course builds on basic principles in biology and microbiology. The course assumes a basic understanding of structure, composition and properties of soils and natural waters. We recommend the following background:
- Basic university course in general chemistry
- Course on soil or geochemistry, e.g. "Soil, Water and Plants"
- Basic university course in Microbiology
For students who are weak within one or more of the basic disciplines we offer short brush-up lectures incl. reading/training.

This the course for those students who:
- are interested in applying chemistry and microbiology to pollutant fate in soils, sediments and natural waters
- would like hands on and experience with computational approaches
- seeks to learn tools that can quantify pollutant formulation, bonding, and degradation, and who would like to use this insight for remediation
- like to work in a class of international students

7,5 ECTS
Type of assessment
Written examination, 4 h under invigilation
Written assignment
Exam comprise project report (counts by 40 %) and a written exam (60 %)
All aids allowed

NB: If the exam is held at the ITX, the ITX will provide computers. Private computer, tablet or mobile phone CANNOT be brought along to the exam. Books and notes should be brought on paper or saved on a USB key.

Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examinator
Criteria for exam assessment

See learning outcome

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 28
  • Theory exercises
  • 32
  • Project work
  • 60
  • Excursions
  • 4
  • Preparation
  • 78
  • Exam
  • 4
  • English
  • 206