The uncontrolled invasive spread of exotic Acacias is a growing concern for many tropical ecosystems, particularly due to their negative impact upon nutrient cycling. Studies investigating the effects of Acacia invasion on nutrient cycling have focused on litterfall and litter decomposition, although its impact on ion deposition in tropical ecosystems is less understood. We quantified and compared the rates of ion deposition (Ca2+, Mg2+, NH4+, NO3−) between Acacia-invaded and non-invaded tropical heath (Kerangas) forest sites in Brunei Darussalam, Southeast Asia. Ion exchange resin (IER) sampler, IER ring and IER bags were used to determine ion depositions via throughfall, in soils and in stream water respectively. Throughfall in Acacia-invaded heath forest sites recorded significantly higher NH4+ and Ca2+ depositions but lower Mg2+ than non-invaded, intact sites. For ion deposition in soil, all depths recorded significantly higher Ca2+ (except for 0 cm depth), Mg2+ and NH4+ depositions, but significantly lower NO3− depositions, in Acacia-invaded sites. Ion deposition in stream water showed significant monthly variations, with Acacia-invaded sites recording significantly higher Mg2+ depositions in June, August and September 2015 but lower NH4+ depositions in June, July and September, lower NO3− and Ca2+ depositions in June and September than non-invaded heath forest sites. Overall, these findings demonstrate that ion deposition via throughfall, in soil and in stream water were all affected by Acacia invasion, thus confirming the influence of alien invasive Acacias on nutrient cycling of tropical heath forests.