Evapotranspiration (ET) plays a crucial role in integrated water resources planning, development and management, especially in tropical and arid regions. Determining ET is not straightforward due to the heterogeneity and complexity found in real-world hydrological basins. This situation is often compounded in regions with limited hydro-meteorological data that are facing rapid development of irrigated agriculture. Remote sensing (RS) techniques have proven useful in this regard. In this study, we compared the daily actual ET estimates derived from 3 remotely-sensed surface energy balance (SEB) models, namely, the Surface Energy Balance Algorithm for Land (SEBAL) model, the Operational Simplified Surface Energy Balance (SSEBop) model, and the Simplified Surface Balance Index (S-SEBI) model. These products were generated using the Moderate Resolution Imaging Spectroradiometer (MODIS) satellite imagery for a total of 44 satellite overpasses in 2005, 2010, and 2015 in the heterogeneous, highly-utilized, rapidly-developing and data-limited Kilombero Valley (KV) river basin in Tanzania, eastern Africa. Our results revealed that the SEBAL model had a relatively high ET compared to other models and the SSEBop model had relatively low ET compared to the other models. In addition, we found that the S-SEBI model had a statistically similar ET as the ensemble mean of all models. Further comparison of SEB models’ ET estimates across different land cover classes and different spatial scales revealed that almost all models’ ET estimates were statistically comparable (based on the Wilcoxon’s test and the Levene’s test at a 95% confidence level), which implies fidelity between and reliability of the ET estimates. Moreover, all SEB models managed to capture the two spatially-distinct ET regimes in KV: the stable/permanent ET regime on the mountainous parts of the KV and the seasonally varied ET over the floodplain which contains a Ramsar site (Kilombero Valley Floodplain). Our results have the potential to be used in hydrological modelling to explore and develop integrated water resources management in the valley. We believe that our approach can be applied elsewhere in the world especially where observed meteorological variables are limited.