In variable light environments, plants rapidly adjust photosynthesis for an optimal balance between photochemistry and photoprotection. There is increasing evidence that ion fluxes across thylakoid membranes play an important role in regulation of photosynthesis. Recent publications from our laboratory have unraveled the roles of the K+/H+ antiporter KEA3, the putative Cl− channel CLCe and the voltage-dependent Cl− channel VCCN1 in thylakoid ion homeostasis and photosynthetic regulation in Arabidopsis thaliana. However, the current knowledge about these transport proteins comes from the characterization of single loss-of-function mutants of the corresponding genes in Arabidopsis, which do not provide information about possible functional relationships between K+ and Cl− fluxes in the thylakoid membrane. In my seminar, I will provide an overview of the current knowledge about genes involved in ion fluxes and regulation of photosynthesis and present data from characterization of double mutants of KEA3, CLCe and VCCN1. Our findings contribute to understanding the thylakoid network of ion fluxes and how they help plants to adjust photosynthesis in variable light environments.