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 pre-kill 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 long-term lake restoration is to be achieved. Our research highlights the enormous potential of multi-indicator palaeolimnology and alludes to an important need to consider potential fish kill signatures when interpreting results.