Multiple stressors affect water quality and biodiversity in lakes worldwide. However, our understanding of which combinations of stressors are of greatest impact and how lakes have shifted from their pre-industrial baselines is fragmented. Questions remain regarding how multiple trophic groups are affected by global change stressors and whether region-specific differences need to be considered. Here, we apply multiple factor analyses together with latent variable modeling to quantify potential interactions within and among taxa that span multiple trophic levels (i.e. diatoms, cladocerans and chironomids) to improve our understanding of paleo-environmental dynamics from a suite of Canadian lakes spanning four ecozones: the Boreal Shield, the Mixedwood Plains, the Atlantic Highlands, and the Atlantic Maritimes. Across all ecozones, multi-trophic assemblages were distinguished in a multiple factor analysis along a land-use gradient, with mesotrophic/eutrophic diatoms and profundal chironomids tolerant of low bottom-water oxygen concentrations recorded in more disturbed sites. Functional units across three indicator groups formed distinct networks of co-responses to key environmental and land-use gradients, although cladocerans seemed to be driven by additional (i.e., residual) gradients. Applying a temporal beta-diversity approach between modern and pre-industrial assemblages, we detected significantly greater turnover of diatom functional groups in high versus low human impact sites (p = 0.03, n = 57), with similar but non-significant trends apparent with the chironomid and cladoceran groups. Ecozonal differences in temporal turnover were also evident in diatom (p = 0.003, n = 57) and chironomid functional groups (p = 0.04, n = 41). The ecozonal differences may be partially due to differential sensitivities of the pre-industrial assemblages and may also be driven by historical disturbances. Our work highlights how the magnitude and direction of ecological change vary across ecozones and can modify responses to human impacts, with a general trend of higher species turnover in sites with greater human disturbance.