This study compares LSTM neural network and wavelet neural network (WNN) for spatio-temporal prediction of rainfall and runoff time-series trends in scarcely gauged hydrologic basins. Using long-term in situ observed data for 30 years (1980–2009) from ten rain gauge stations and three discharge measurement stations, the rainfall and runoff trends in the Nzoia River basin are predicted through satellite-based meteorological data comprising of: precipitation, mean temperature, relative humidity, wind speed and solar radiation. The prediction modelling was carried out in three sub-basins corresponding to the three discharge stations. LSTM and WNN were implemented with the same deep learning topological structure consisting of 4 hidden layers, each with 30 neurons. In the prediction of the basin runoff with the five meteorological parameters using LSTM and WNN, both models performed well with respective R2 values of 0.8967 and 0.8820. The MAE and RMSE measures for LSTM and WNN predictions ranged between 11–13 m3/s for the mean monthly runoff prediction. With the satellite-based meteorological data, LSTM predicted the mean monthly rainfall within the basin with R2 = 0.8610 as compared to R2 = 0.7825 using WNN. The MAE for mean monthly rainfall trend prediction was between 9 and 11 mm, while the RMSE varied between 15 and 21 mm. The performance of the models improved with increase in the number of input parameters, which corresponded to the size of the sub-basin. In terms of the computational time, both models converged at the lowest RMSE at nearly the same number of epochs, with WNN taking slightly longer to attain the minimum RMSE. The study shows that in hydrologic basins with scarce meteorological and hydrological monitoring networks, the use satellite-based meteorological data in deep learning neural network models are suitable for spatial and temporal analysis of rainfall and runoff trends.