Van Niekerk is a CSIR senior researcher in the urban and regional planning group. The group consists of urban planners, geographers, modellers and geo-information specialists who conduct research into urban spatial change phenomena with a view to inform urban spatial planning and policy in cities and regions of South Africa.

A professional planner, Van Niekerk is involved in projects related to spatial and demographic trends analyses, urban disaster risk reduction, urban climate change adaptation, planning and design guidelines, infrastructure investment priorities, and spatial alignment and planning. She is the project manager for the Green Book project, a multidisciplinary, three-year project to write planning and design guidelines for adapting South African settlements to climate change. Van Niekerk is also active in the dissemination of research results through training, conference papers, articles for web portals, book chapters, policy notes and journal articles.