Methods, systems, and media for generating modified user engagement signals based on obstructed layers in a user interface are provided. In some embodiments, the method includes: identifying a plurality of layers in a user interface, wherein each layer in the plurality of layers has a layer depth value, and wherein the plurality of layers are presented in an order based on the layer depth value associated with each layer; selecting a first layer in the plurality of layers as a reference layer; determining a plurality of layer components from a remaining subset of layers in the plurality of layers, wherein the plurality of layer components results in at least one hidden component, wherein the at least one hidden component is a portion of the reference layer that is prevented from being viewed by a user of the user interface when the plurality of layer components is presented in the order indicated by the layer depth value of each layer; associating the plurality of layer components with an obstruction database for the reference layer; and generating, from a user engagement signal, a modified user engagement signal by identifying, using the obstruction database, a portion of the user engagement signal that is based on the at least one hidden component and removing the portion of the user engagement signal that is based on the at least one hidden component.