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The Indicators of Hydrologic Alteration (IHA) based on 33 parameters in five dimensions (flow magnitude, timing, duration, frequency and change rate) have been widely used in evaluation of hydrologic alteration in river systems. Yet, inter-correlation seriously exists amongst those parameters, therefore constantly underestimates or overestimates actual hydrological changes. Toward the end, a new method (Representative-IHA, RIHA) is developed by removing repetitions based on Criteria Importance Through Intercriteria Correlation (CRITIC) algorithm. RIHA is testified in evaluating effects of future climate change on hydro-ecology in the Niger River of Africa. Future flows are projected using three watershed hydrological models forced by five general circulation models (GCMs) under three Representative Concentration Pathways (RCPs) scenarios. Results show that: (1) RIHA is able to eliminate self-correlations amongst IHA indicators and identify the dominant characteristics of hydrological alteration in the Upper Niger River, (2) March streamflow, September streamflow, December streamflow, 30-day annual maximum, low pluses duration and fall rates tends to increase over the period 2010–2099, while July streamflow and 90-day annual minimum streamflow shows decrease, (3) the Niger River will undergo moderate flow alteration under RCP8.5 in 2050s and 2080s and low alteration other scenarios, (4) future flow alteration may induce increase water temperatures, reduction dissolved oxygen and food resources. Consequently, aquatic biodiversity and fish community of Upper Niger River would become more vulnerable in the future. The new method enables more scientific evaluation for multi-dimensional hydrologic alteration under the context of climate change. [ABSTRACT FROM AUTHOR]