Human action and perception are dependent upon continuous interactions between the brain, the body, and the environment. Our expectations of how to function in the world around us are largely determined by affordances within our environment and our bodies, and when our predictions are disturbed or perturbed, we need to determine how to behave in a novel and adaptive way given a new set of affordances. In this dissertation, I examine different ways in which the brain and body respond to perturbations from the environment by studying these perturbations effects on behavior. In the first chapter, I conducted a study to determine how humans respond to sequences of auditory and visual stimuli, and how errors in their timing to stimuli are corrected by one’s own movement. In the second chapter, I investigate how the human body, specifically the arms, responds to drastic changes in haptic sensation using elastic and viscous forces on the hands during reaching movements. The third chapter extends the definition of perturbation to include exogenous perturbations to the brain using transcranial magnetic stimulation. The motor cortex and posterior parietal cortex were modulated to be less responsive during consolidation of motor and declarative skills, and I examined how participants used different strategies to adapt to this perturbation. In the fourth chapter, I used meta-analytic methods to determine what, if any, commonalities exist among participants who received perturbations using facilitatory transcranial magnetic stimulation to the brain to determine if this method enhances cognition. This work is intended to add further insight into the connections between the human brain and body, and how we respond behaviorally when perturbations are introduced to our systems, which include the environment we operate in. This dissertation, Perturbations to cognitive systems and downstream effects on behavior, is submitted by Alexandria Pabst in the summer of 2021 in partial fulfillment of the degree Doctor of Philosophy in Cognitive and Information Sciences at the University of California, Merced, under the guidance of Ramesh Balasubramaniam.