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This paper reports on the energy balance and partitioning analysed from 3-year micrometeorological flux measurements of energy and water fluxes over a heterogeneous semi-arid shrubland ecosystem in Lake Naivasha basin. The measurements enabled the characterization of the seasonal and interannual variability of the energy and water fluxes of the ecosystem covering two wet years (2012 and 2013) and one drought year (2014). On an annual scale, more than 60% of net radiation (Rn) was partitioned as latent (LE) and sensible (H) energy flux, with the latter being the larger consumer of Rn (similar to 34%) and dominant for most months. The transition from H to LE dominance occurred from early noon to late afternoon in the wettest months of April and May. The residual energy balance closure term (C) accounted for between 25 and 40% of the Rn with the imbalance tending to be highest during periods of high insolation. Annual evapotranspiration was estimated at 873 mm, 632mm and 537mm for year 2012, 2013 and 2014 respectively. This accounted for at least 80% of the annual precipitation received for the respective years. Surface conductance (g(s)) scaled significantly with leaf expansion and Priestley-Taylor alpha coefficient, but was limited during periods of drought because of inadequate soil moisture suggesting that, change in LE was paralleled by changes in green leaf area index. Low values of decoupling coefficient (Omega) during these periods indicated that evapotranspiration was strongly controlled by g(s) and vapour pressure deficit (VPD). However, under non-limiting moisture conditions evapotranspiration was decoupled from the atmosphere. This suggested that during the dry seasons and periods of prolonged drought, a lack of moisture in combination with high VPD leads to significant decreases in stomatal conductance that eventually limits partitioning of available energy into LE in the semi-arid ecosystem part of the Lake Naivasha basin. However, during wet season these factors are non-limiting and radiation is the dominant control of energy partitioning into LE in the ecosystem. The coupling and decoupling pattern provide insights towards formulating models that quantify evapotranspiration for ecosystems that experience seasonal shifts in controlling factors. Copyright (C) 2016 John Wiley & Sons, Ltd.