Measurement of human body movement is an essential step in biomechanical analysis. The current standard for human motion capture systems uses infrared cameras to track reflective markers placed on the subject. While these systems can accurately track joint kinematics, the analyses are spatially limited to the lab environment. Though Inertial Measurement Unit (IMU) can eliminate the spatial limitations of the motion capture system, those systems are impractical for use in daily living due to the need for many sensors, typically one per body segment. Due to the need for practical and accurate estimation of joint kinematics, this study implements a reduced number of IMU sensors and employs machine learning algorithm to map sensor data to joint angles. Our developed algorithm estimates hip, knee, and ankle angles in the sagittal plane using two shoe-mounted IMU sensors in different practical walking conditions: treadmill, level overground, stair, and slope conditions. Specifically, we proposed five deep learning networks that use combinations of Convolutional Neural Networks (CNN) and Gated Recurrent Unit (GRU) based Recurrent Neural Networks (RNN) as base learners for our framework. Using those five baseline models, we proposed a novel framework, DeepBBWAE-Net, that implements ensemble techniques such as bagging, boosting, and weighted averaging to improve kinematic predictions. DeepBBWAE-Net predicts joint kinematics for the three joint angles under all the walking conditions with a Root Mean Square Error (RMSE) 6.93-29.0% lower than base models individually. This is the first study that uses a reduced number of IMU sensors to estimate kinematics in multiple walking environments.