Aquatic ecosystems have shifted from prehistoric baseline states due to anthropogenic and environmental change, but we generally lack long-term data to understand such change particularly in marine and freshwater systems. Fish are excellent, and largely underused proxies for elucidating the degree, direction and scale of shifts in aquatic ecosystems. Much qualitative and quantitative data can be derived from contemporary, archived and ancient sources. Archives of calcified structures along with modern day samples provide an alternative resource whereby long-term data can be generated in a relatively cheap and cost-effective manner. Such samples provide data on biological, ecological and environmental baseline shifts. Several species will be used to show how the abundance, size and age structure, growth and environment inhabited by fish has changed over decadal and centennial time scales. Understanding biological responses to ecosystem change is useful for developing effective management and conservation strategies.