Emerging aquatic insects serve as one link between aquatic and adjacent riparian food webs via the flux of energy and nutrients. These insects provide high-quality subsidy to terrestrial predators. Thus, any disturbance of emergence processes may cascade to higher trophic levels and lead to effects across ecosystem boundaries. One stressor with potential impact on non-target aquatic insects, especially on non-biting midges (Diptera: Chironomidae), is the widely used mosquito control agent Bacillus thuringiensis var. israelensis (Bti). In a field experiment, we investigated emerging insect communities from Bti-treated (three applications, maximum field rate) and control floodplain pond mesocosms (FPMs) over 3.5 months for changes in their composition, diversity as well as the emergence dynamics and the individual weight of emerged aquatic insects over time. Bti treatments altered community compositions over the entire study duration – an effect mainly attributed to an earlier (∼10 days) and reduced (∼26%) peak in the emergence of Chironomidae, the dominant family (88% of collected individuals). The most reasonable explanation for this significant alteration is less resource competition caused by a decrease in chironomid larval density due to lethal effects of Bti. This is supported by the higher individual weight of Chironomidae emerging from treated FPMs (∼21%) during Bti application (April – May). A temporal shift in the emergence dynamics can cause changes in the availability of prey in linked terrestrial ecosystems. Consequently, terrestrial predators may be affected by a lack of appropriate prey leading to bottom-up and top-down effects in terrestrial food webs. This study indicates the importance of a responsible and elaborated use of Bti and additionally, highlights the need to include a temporal perspective in evaluations of stressors in aquatic-terrestrial meta-ecosystems. Display omitted •Study on insect emergence from natural floodplain pond mesocosms stressed by Bti.•Temporal dynamics of emerging insects changed significantly.•Emergence of Chironomidae peaked 10 days earlier and was substantially reduced.•Larval mortality is assumed to increase resource availability explaining the results.•Altered aquatic subsidy may cascade to terrestrial predators in sensitive life phases.