Precise estimation of physical hydrology components including groundwater levels (GWLs) is a challenging task, especially in relatively non-contiguous watersheds. This study estimates GWLs with deep learning and artificial neural networks (ANNs), namely a multilayer perceptron (MLP), long short term memory (LSTM), and a convolutional neural network (CNN) with four different input variable combinations for two watersheds (Baltic River and Long Creek) in Prince Edward Island, Canada. Variables including stream level, stream flow, precipitation, relative humidity, mean temperature, evapotranspiration, heat degree days, dew point temperature, and evapotranspiration for the 2011-2017 period were used as input variables. Using a hit and trial approach and various hyperparameters, all ANNs were trained from scratched (2011)(2012)(2013)(2014)(2015) and validated (2016)(2017). The stream level was the major contributor to GWL fluctuation for the Baltic River and Long Creek watersheds (R 2 = 50.8 and 49.1%, respectively). The MLP performed better in validation for Baltic River and Long Creek watersheds (RMSE = 0.471 and 1.15, respectively). Increased number of variables from 1 to 4 improved the RMSE for the Baltic River watershed by 11% and for the Long Creek watershed by 1.6%. The deep learning techniques introduced in this study to estimate GWL fluctuations are convenient and accurate as compared to collection of periodic dips based on the groundwater monitoring wells for groundwater inventory control and management.Water 2020, 12, 5 2 of 18 procedure that requires thorough knowledge of physical hydrological parameters, big data, hydrological models, model inputs, and the geometry of watersheds [3]. Aspects of hydrogeology-i.e., geological factors affecting the distribution and movement of groundwater underneath the soil surface-need to be properly understood when modeling GWLs and manipulating the modeling results. Watershed scale fluctuations in GWLs occur over a period of several decades, and the resulting cumulative effects on streamflow depletion may not be fully realized for years [4]. Resultantly, depending upon the distance of the pumping station from the stream and the geologic characteristics of the aquifer, the groundwater system may take decades to recover from streamflow depletion caused by intermittent pumping. Components of the surface-and the sub-surface physical hydrology of a watershed-i.e., streamflow and groundwater flow, respectively-are interconnected, making the stream-aquifer interaction one of the key processes governing the groundwater flow pattern in a watershed [1]. Groundwater fluctuations affect streamflow and vice versa, as the pumping wells capture groundwater that would otherwise discharge to connected streams, rivers, and other surface-water bodies [4]. Francis [5] reported that, in typical watersheds of Prince Edward Island, the base flow represents almost 80% of the streamflow in the late summer and fall months. Stream length in these island watersheds ranges from less than 1 km to 2...