Water scarcity can intensify streamflow reduction, alter hydromorphology, increase chemical pollution, and disrupt resource exchange between aquatic and terrestrial ecosystems. However, the effects of streamflow reduction on pesticide concentrations in sediment, and how these changes influence aquatic insect emergence and riparian spider communities, remain poorly understood. We conducted a 39-day mesocosm experiment in Southwest Germany using 12 artificial stream mesocosm with adjacent riparian areas, randomly assigned to low-flow (0.4 L s−1) treatment or control (1 L s−1) to simulate flow alteration. We sampled water daily (47 days), sediment (weeks 4 and 6), emerging insects (weekly for 5 weeks), and riparian spiders (week 6). Our results show that under low-flow conditions, the mean sediment pesticide concentrations increased slightly stronger from week 4 to week 6, compared to the control. However, the high variability within treatments resulted in no significant differences between the treatments. Low flow caused a 2.9-fold reduction in the total abundance of Ephemeroptera, Plecoptera, and Trichoptera (EPT), while total emerging insects (abundance and biomass) and spider abundance were not affected significantly. However, the web-building spider Tetragnatha sp. was 2.6-fold less abundant under low-flow conditions, likely due to vegetation–habitat-related responses and reduced EPT abundance, while the ground-hunting Lycosidae were unaffected, owing to their active hunting behavior and generalist strategy. These findings highlight the need to consider cross-ecosystem effects when assessing the ecological impacts of hydrological alterations in contaminated aquatic ecosystems.