Fish kills are a common occurrence in shallow, eutrophic lakes, but their ecological consequences, especially in the long term, are poorly understood. We studied the decadal-scale response of two UK shallow lakes to fish kills using a palaeolimnological approach. Eutrophic and turbid Barningham Lake experienced two fish kills in the early 1950s and late 1970s with fish recovering after both events, whereas less eutrophic, macrophyte-dominated Wolterton Lake experienced one kill event in the early 1970s from which fish failed to recover. Our palaeo-data show fish-driven trophic cascade effects across all trophic levels (covering benthic and pelagic species) in both lakes regardless of prekill macrophyte coverage and trophic status. In turbid Barningham Lake, similar to long-term studies of biomanipulations in other eutrophic lakes, effects at the macrophyte level are shown to be temporary after the first kill (c. 20 years) and non-existent after the second kill. In plant-dominated Wolterton Lake, permanent fish disappearance failed to halt a long-term pattern of macrophyte community change (for example, loss of charophytes and over-wintering macrophyte species) symptomatic of eutrophication. Important implications for theory and restoration ecology arise from our study. Firstly, our data support ideas of slow eutrophication-driven change in shallow lakes where perturbations are not necessary prerequisites for macrophyte loss. Secondly, the study emphasises a key need for lake managers to reduce external nutrient loading if sustainable and longterm lake restoration is to be achieved. Our research highlights the enormous potential of multiindicator palaeolimnology and alludes to an important need to consider potential fish kill signatures when interpreting results.