A thesis on climate change and its effects could focus on a particular region and examine both recorded and projected impact on the land. Propose or design a system for your thesis which tracks changes in surface temperature, underground lakes, soil quality and so on. Explore how climate change has affected these elements, and what future impact can be predicted. You can look at previous studies by climate scientists and organizations such as the climate institute.
Pinpoint a specific business which already uses GIS; for example, a mining company that measures underground water resources or mining deposits. Your thesis could determine how certain companies are using this technology and if it is proving effective. Expand on this by discussing how GIS technology could be better utilized by industry or how GIS results can be submitted to governments to monitor companies' environmental impact.
In the last few years the planet has been plagued by earthquakes, tidal waves and other natural disasters. Design a GIS that would calculate the damage these events inflict on an area. This could be used both to predict and to prevent damage to certain structures and areas. You could focus on one particular city or on a range of areas. For example, examine an area hit by an earthquake to determine the frequency of landslides in the region, what type of structures suffered the most damage, and so on.
GIS has long been used by archaeologists in their search for ancient artifacts buried deep below the surface. Look at ways this technology could be further developed. In particular, explore how it can be combined with global positioning satellites and multi-beam echo sounders to find artifacts much deeper below ground level and even under the sea.