AbstractThe effects of long‐term atmospheric deposition of pollutant elements on the trans‐surface causative relationships at three lake sites having different catchment characteristics were investigated in this study. The selected determinants included lake productivity, bottom sediment quality, and a suite of microbial variables (microbial biomass (Cmic); basal respiration; substrate‐induced respiration; bacterial:fungal ratio; metabolic quotient; and alkaline phosphatase and FDAase activities) measured at the land–water interface, in relation to atmospheric deposition of phosphate; nitrate; ammonium; sulphate; calcium; and magnesium. The results indicated significant between‐site differences (P < 0.001) in the atmospheric deposition of phosphate (0.21–1.96 kg.h−1.year−1); nitrate (2.77–28.05 kg.h−1.year−1); ammonium (0.58–11.60 kg.h−1.year−1); sulphate (5.64–32.15 kg.h−1.year−1); calcium (4.50–30.00 kg.h−1.year−1); and magnesium (1.50–12.15 kg.h−1.year−1), as well as a consistently increasing input of these ions across time. The catchment vegetation had important effects on microbial variables that, in turn, affected lake productivity. Interfaces of woodland lake were found to be rich in phenolics, supporting low Cmic and activities. Except for alkaline phosphatase, which declined over time, atmospheric deposition of pollutant elements increased the Cmic and activities at the land–water interface. The time lag correlation analysis indicated the Cmic and lake productivity relationships were significantly altered by atmospherically driven nitrogen and phosphorus inputs, with a time lag of 2–3 years. Despite being supportive, aerial nutrient inputs appeared to have a destabilizing effect on both, microbial biomass and lake productivity variables. These observations indicate that if present atmospheric deposition trends of pollutant elements continue, it will modify the cross‐domain causative relationships of inland lentic systems over the long term. These study results are relevant for the formulation of strategies for managing freshwater tropical lakes.