Webber's previous research interests have focused on the molecular mechanisms of photosynthetic energy transduction and chloroplast development. A long-standing project has focused on the structure and function of the photosystem I reaction center complex. The structure of photosystem I is now known at atomic resolution. However, it is still unknown why the electron transfer cofactors have such a remarkably low potential.

His research has used recombinant DNA techniques to specifically alter the genes encoding the photosystem I heterodimer to understand how the protein environment modulates essential physico-chemical properties of the electron transfer intermediates. The eukaryotic green alga Chlamydomonas reinhardtii was used as a model organism in these studies. The chloroplast genome of Chlamydomonas were transformed using a "gene gun" to shoot modified genes, carried on sub-micron sized gold particles, into the chloroplast. Mutant cells were produced that synthesize the reaction-center complex with altered polypeptide components. These site-specific mutants of Chlamydomonas were characterized using a range of molecular, biochemical and biophysical techniques. Recently, Webber's research focus has shifted to algal biotechnology and the use of algae for waste water purification and production of useful byproducts.  Many genetic engineering approaches that were applied to his previous research are being used for these new endeavors.