Species declines due to changing environmental conditions or anthropogenic influences such as fisheries harvest as well as species introductions probably have consequences beyond the species by also altering their food webs. The scope of the effect on the structure and function of aquatic ecosystems likely depends on the role of the affected species (e.g., grazer/consumer, ecosystem engineer, keystone species) and on the spatial and temporal scale considered. Spatial effects can be fairly small, like the introduction of a species in an individual pond or lake, or relatively large, like the decline of anadromous fish migrations affecting thousands of kilometers. Temporal effects may be short-term, such as loss of species due to drought which may be replenished from nearby source populations following rewetting, or long-term, such as the installation of a dam that alters natural flow and temperature regimes of rivers. Ultimately, to gain a better understanding of the implications of food web alterations, the potential pathways of influence need to be explicitly considered across various spatial and temporal scales to identify the challenges aquatic ecosystems face.